Hackseq scripts:

@sjackman could you please look at scripts:

This one for creation containers manually:

NAME=$(id -un)_$UID
USER=$(id -un)
CONTAINER_HOSTNAME=$(id -un)-ORCA
LOG_FILE=/orca_repo/access_log/docker_login.log
FILES_LOCATION=/orca_repo/etc

PROJECT=project1


docker run -t --name $PROJECT -m 100GB --memory-reservation 20GB -v /etc/hosts:/etc/hosts:ro -v /projects/hackathon/2017/$PROJECT:/home/$PROJECT -v $FILES_LOCATION/passwd:/etc/passwd:ro -v $FILES_LOCATION/group:/etc/group:ro -w /home/hackseq17 -v /home/hackseq17:/home/hackseq17 -v /tmp/.X11-unix:/tmp/.X11-unix --net host bcgsc/orca-hackseq:2017.10.12

This one is log in:
https://github.com/bcgsc/orca/blob/master/scripts/orca.hackton

poretools

==> Using Homebrew-provided fortran compiler.
This may be changed by setting the FC environment variable.
==> Downloading https://github.com/arq5x/poretools/archive/v0.6.0.tar.gz
==> Downloading from https://codeload.github.com/arq5x/poretools/tar.gz/v0.6.0
######################################################################## 100.0%
==> Downloading https://files.pythonhosted.org/packages/c6/fe/97319581905de40f1be7015a0ea1bd336a756f6249914b148a17eefa75dc/Cython-0.24.1.tar.gz
######################################################################## 100.0%
==> python -c import setuptools... --no-user-cfg install --prefix=/tmp/poretools-20170816-16741-dgiq70/poretools-0.6.0/cython --single-version-externally-managed --record=in
^[[B==> Downloading https://files.pythonhosted.org/packages/d4/0c/9840c08189e030873387a73b90ada981885010dd9aea134d6de30cd24cb8/virtualenv-15.1.0.tar.gz
######################################################################## 100.0%
==> python -c import setuptools... --no-user-cfg install --prefix=/tmp/poretools--homebrew-virtualenv-20170816-16741-1t5oaul/target --single-version-externally-managed --rec
==> python -s /tmp/poretools--homebrew-virtualenv-20170816-16741-1t5oaul/target/bin/virtualenv -p python /home/linuxbrew/.linuxbrew/Cellar/poretools/0.6.0_5/libexec
==> Downloading https://files.pythonhosted.org/packages/b3/b2/238e2590826bfdd113244a40d9d3eb26918bd798fc187e2360a8367068db/six-1.10.0.tar.gz
######################################################################## 100.0%
==> /home/linuxbrew/.linuxbrew/Cellar/poretools/0.6.0_5/libexec/bin/pip install -v --no-deps --no-binary :all: --ignore-installed /tmp/poretools--six-20170816-16741-1iaz3u2/
==> Downloading https://files.pythonhosted.org/packages/e0/4c/515d7c4ac424ff38cc919f7099bf293dd064ba9a600e1e3835b3edefdb18/numpy-1.11.1.tar.gz
######################################################################## 100.0%
==> /home/linuxbrew/.linuxbrew/Cellar/poretools/0.6.0_5/libexec/bin/pip install -v --no-deps --no-binary :all: --ignore-installed /tmp/poretools--numpy-20170816-16741-1ixkh4
==> Downloading https://files.pythonhosted.org/packages/c2/4b/137dea450d6e1e3d474e1d873cd1d4f7d3beed7e0dc973b06e8e10d32488/cycler-0.10.0.tar.gz
######################################################################## 100.0%
==> /home/linuxbrew/.linuxbrew/Cellar/poretools/0.6.0_5/libexec/bin/pip install -v --no-deps --no-binary :all: --ignore-installed /tmp/poretools--Cycler-20170816-16741-5wuk3
==> Downloading https://files.pythonhosted.org/packages/22/82/64dada5382a60471f85f16eb7d01cc1a9620aea855cd665609adf6fdbb0d/h5py-2.6.0.tar.gz
######################################################################## 100.0%
==> /home/linuxbrew/.linuxbrew/Cellar/poretools/0.6.0_5/libexec/bin/pip install -v --no-deps --no-binary :all: --ignore-installed /tmp/poretools--h5py-20170816-16741-1ib5exy
Last 15 lines from /home/linuxbrew/.cache/Homebrew/Logs/poretools/07.pip:
  Removing source in /tmp/pip-TW4Pws-build
Command "/home/linuxbrew/.linuxbrew/Cellar/poretools/0.6.0_5/libexec/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-TW4Pws-build/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-BN20bc-record/install-record.txt --single-version-externally-managed --compile --install-headers /home/linuxbrew/.linuxbrew/Cellar/poretools/0.6.0_5/libexec/include/site/python2.7/h5py" failed with error code 1 in /tmp/pip-TW4Pws-build/
Exception information:
Traceback (most recent call last):
  File "/home/linuxbrew/.linuxbrew/lib/python2.7/site-packages/pip/basecommand.py", line 215, in main
    status = self.run(options, args)
  File "/home/linuxbrew/.linuxbrew/lib/python2.7/site-packages/pip/commands/install.py", line 342, in run
    prefix=options.prefix_path,
  File "/home/linuxbrew/.linuxbrew/lib/python2.7/site-packages/pip/req/req_set.py", line 784, in install
    **kwargs
  File "/home/linuxbrew/.linuxbrew/lib/python2.7/site-packages/pip/req/req_install.py", line 878, in install
    spinner=spinner,
  File "/home/linuxbrew/.linuxbrew/lib/python2.7/site-packages/pip/utils/__init__.py", line 707, in call_subprocess
    % (command_desc, proc.returncode, cwd))
InstallationError: Command "/home/linuxbrew/.linuxbrew/Cellar/poretools/0.6.0_5/libexec/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-TW4Pws-build/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-BN20bc-record/install-record.txt --single-version-externally-managed --compile --install-headers /home/linuxbrew/.linuxbrew/Cellar/poretools/0.6.0_5/libexec/include/site/python2.7/h5py" failed with error code 1 in /tmp/pip-TW4Pws-build/

READ THIS: https://github.com/Linuxbrew/brew/blob/master/docs/Troubleshooting.md#troubleshooting
Please do not report this issue to Homebrew/brew or Homebrew/core, which support macOS only.

These open issues may also help:
poretools: Build a bottle for Linuxbrew: h5py: cc: error: unrecognized command line option '-R' https://github.com/Homebrew/homebrew-science/pull/5065 ```

[email protected] fails.

==> Installing [email protected]
==> Downloading https://ftp.gnu.org/gnu/gcc/gcc-4.8.5/gcc-4.8.5.tar.bz2
######################################################################## 100.0%
==> ../configure --build=x86_64-apple-darwin3.10.0-327.el7.x86_64 --prefix=/home/linuxbrew/.linuxbrew/Cellar/[email protected]/4.8.5 
Last 15 lines from /home/linuxbrew/.cache/Homebrew/Logs/[email protected]/01.configure:
--with-system-zlib
--enable-libstdcxx-time=yes
--enable-stage1-checking
--enable-checking=release
--enable-lto
--enable-plugin
--disable-werror
--with-pkgversion=Homebrew GCC 4.8.5
--with-bugurl=https://github.com/Homebrew/homebrew-core/issues
MAKEINFO=missing
--disable-nls
--enable-multilib

checking build system type... Invalid configuration `x86_64-apple-darwin3.10.0-327.el7.x86_64': machine `x86_64-apple-darwin3.10.0-327.el7.x86_64' not recognized
configure: error: /bin/bash ../config.sub x86_64-apple-darwin3.10.0-327.el7.x86_64 failed

BioPerl: FAIL Installing Bio::Root::Version failed

One month ago it worked.

on docker2, run docker run -ti 24b21f10017c
then
cpanm -i Bio::Root::Version

The following log:

cpanm (App::cpanminus) 1.7043 on perl 5.026000 built for x86_64-linux-thread-multi
Work directory is /home/linuxbrew/.cpanm/work/1502408933.12319
You have make /usr/bin/make
You have /usr/bin/curl
You have /bin/tar: tar (GNU tar) 1.27.1
Copyright (C) 2013 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>.
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.

Written by John Gilmore and Jay Fenlason.
Searching Bio::Root::Version () on cpanmetadb ...
--> Working on Bio::Root::Version
Fetching http://www.cpan.org/authors/id/C/CJ/CJFIELDS/BioPerl-1.007001.tar.gz
-> OK
Unpacking BioPerl-1.007001.tar.gz
Entering BioPerl-1.007001
Checking configure dependencies from META.json
Checking if you have ExtUtils::Install 1.46 ... Yes (2.04)
Checking if you have Module::Build 0.42 ... Yes (0.4224)
Configuring BioPerl-1.007001
Running Build.PL
Checking prerequisites...
  recommends:
    *  Algorithm::Munkres is not installed
    *  Array::Compare is not installed
    *  Bio::Phylo is not installed
    *  CGI is not installed
    *  Clone is not installed
    *  Convert::Binary::C is not installed
    *  Error is not installed
    *  GD is not installed
    *  Graph is not installed
    *  GraphViz is not installed
    *  HTML::TableExtract is not installed
    *  IO::Scalar is not installed
    *  Inline::C is not installed
    *  LWP::UserAgent is not installed
    *  PostScript::TextBlock is not installed
    *  SVG is not installed
    *  SVG::Graph is not installed
    *  Set::Scalar is not installed
    *  Sort::Naturally is not installed
    *  Spreadsheet::ParseExcel is not installed
    *  XML::DOM is not installed
    *  XML::DOM::XPath is not installed
    *  XML::LibXML is not installed
    *  XML::Parser is not installed
    *  XML::Parser::PerlSAX is not installed
    *  XML::SAX::Writer is not installed
    *  XML::Simple is not installed
    *  XML::Twig is not installed
    *  XML::Writer is not installed
    *  YAML is not installed

Checking optional features...
EntrezGene............disabled
  requires:
    ! Bio::ASN1::EntrezGene is not installed
Network Tests.........disabled
  requires:
    ! LWP::UserAgent is not installed
Pg Tests..............disabled
  requires:
    ! DBD::Pg is not installed
SQLite Tests..........disabled
  requires:
    ! DBD::SQLite is not installed

ERRORS/WARNINGS FOUND IN PREREQUISITES.  You may wish to install the versions
of the modules indicated above before proceeding with this installation

Do you want to run the Bio::DB::GFF or Bio::DB::SeqFeature::Store live database tests? y/n [n]   - will not run the BioDBGFF or BioDBSeqFeature live database tests

Install [a]ll BioPerl scripts, [n]one, or choose groups [i]nteractively? [a]   - will install all scripts

Created MYMETA.yml and MYMETA.json
Creating new 'Build' script for 'BioPerl' version '1.007001'
-> OK
Checking dependencies from MYMETA.json ...
Checking if you have Module::Build 0.42 ... Yes (0.4224)
Checking if you have CPAN 1.81 ... Yes (2.18)
Checking if you have Scalar::Util 0 ... Yes (1.46_02)
Checking if you have URI::Escape 0 ... Yes (3.31)
Checking if you have Test::Harness 2.62 ... Yes (3.38)
Checking if you have ExtUtils::Manifest 1.52 ... Yes (1.70)
Checking if you have Test::Most 0 ... Yes (0.35)
Checking if you have Data::Stag 0.11 ... Yes (0.14)
Checking if you have IO::String 0 ... Yes (1.08)
Building and testing BioPerl-1.007001
Building BioPerl
t/Align/AlignStats.t ................... ok
t/Align/AlignUtil.t .................... ok
t/Align/Graphics.t ..................... skipped: The optional module GD (or dependencies thereof) was not installed
t/Align/SimpleAlign.t .................. ok
t/Align/TreeBuild.t .................... ok
t/Align/Utilities.t .................... ok
t/AlignIO/AlignIO.t .................... ok
t/AlignIO/arp.t ........................ ok
t/AlignIO/bl2seq.t ..................... ok
t/AlignIO/clustalw.t ................... ok
t/AlignIO/emboss.t ..................... ok
t/AlignIO/fasta.t ...................... ok
t/AlignIO/largemultifasta.t ............ ok
t/AlignIO/maf.t ........................ ok
t/AlignIO/mase.t ....................... ok
t/AlignIO/mega.t ....................... ok
t/AlignIO/meme.t ....................... ok
t/AlignIO/metafasta.t .................. ok
t/AlignIO/msf.t ........................ ok
t/AlignIO/nexml.t ...................... skipped: The optional module Bio::Phylo (or dependencies thereof) was not installed
t/AlignIO/nexus.t ...................... ok
t/AlignIO/pfam.t ....................... ok
t/AlignIO/phylip.t ..................... ok
t/AlignIO/po.t ......................... ok
t/AlignIO/prodom.t ..................... ok
t/AlignIO/psi.t ........................ ok
t/AlignIO/selex.t ...................... ok
t/AlignIO/stockholm.t .................. ok
t/AlignIO/xmfa.t ....................... ok
t/Alphabet.t ........................... ok
t/Annotation/Annotation.t .............. ok
t/Annotation/AnnotationAdaptor.t ....... ok
t/Assembly/ContigSpectrum.t ............ ok
t/Assembly/IO/bowtie.t ................. skipped: The optional module Bio::DB::Sam (or dependencies thereof) was not installed
t/Assembly/IO/sam.t .................... skipped: The optional module Bio::DB::Sam (or dependencies thereof) was not installed
t/Assembly/core.t ...................... ok
t/Cluster/UniGene.t .................... ok
t/ClusterIO/ClusterIO.t ................ ok
t/ClusterIO/SequenceFamily.t ........... ok
t/ClusterIO/unigene.t .................. ok
t/Draw/Pictogram.t ..................... skipped: The optional module SVG (or dependencies thereof) was not installed
t/LiveSeq/Chain.t ...................... ok
t/LiveSeq/LiveSeq.t .................... ok
t/LiveSeq/Mutation.t ................... ok
t/LiveSeq/Mutator.t .................... ok
File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at Bio/DB/GFF.pm line 2000.

You are loading a Bio::DB::GFF database with GFF3 formatted data.
While this will likely work fine, the Bio::DB::GFF schema does not
always faithfully capture the complexity represented in GFF3 files.
Unless you have a specific reason for using Bio::DB::GFF, we suggest
that you use a Bio::DB::SeqFeature::Store database and its corresponding
loader, bp_seqfeature_load.pl.

t/LocalDB/BioDBGFF.t ................... ok
BDB1557 library build did not include support for cryptography
: No such file or directory

------------- EXCEPTION -------------
MSG: Could not open index file /tmp/NsAzDID6hk/dbfa/directory.index: No such file or directory
STACK Bio::DB::IndexedBase::_open_index Bio/DB/IndexedBase.pm:712
STACK Bio::DB::IndexedBase::_index_files Bio/DB/IndexedBase.pm:689
STACK Bio::DB::IndexedBase::index_dir Bio/DB/IndexedBase.pm:487
STACK Bio::DB::IndexedBase::new Bio/DB/IndexedBase.pm:402
STACK toplevel t/LocalDB/Fasta.t:27
-------------------------------------

# Looks like your test exited with 2 before it could output anything.
t/LocalDB/Fasta.t ...................... 
Dubious, test returned 2 (wstat 512, 0x200)
Failed 109/109 subtests 
BDB1557 library build did not include support for cryptography
: No such file or directory

------------- EXCEPTION -------------
MSG: Could not open primary index file: No such file or directory (did you remember to use -write_flag=>1?)
STACK Bio::DB::Flat::BDB::_open_bdb Bio/DB/Flat/BDB.pm:435
STACK Bio::DB::Flat::BDB::primary_db Bio/DB/Flat/BDB.pm:417
STACK Bio::DB::Flat::BDB::_store_primary Bio/DB/Flat/BDB.pm:352
STACK Bio::DB::Flat::BDB::_store_index Bio/DB/Flat/BDB.pm:338
STACK Bio::DB::Flat::BDB::_index_file Bio/DB/Flat/BDB.pm:249
STACK Bio::DB::Flat::BDB::build_index Bio/DB/Flat/BDB.pm:228
STACK toplevel t/LocalDB/Flat.t:30
-------------------------------------

# Looks like your test exited with 2 just after 2.
t/LocalDB/Flat.t ....................... 
Dubious, test returned 2 (wstat 512, 0x200)
Failed 23/25 subtests 
BDB1557 library build did not include support for cryptography
: No such file or directory

------------- EXCEPTION -------------
MSG: Can't open 'DB_File' dbm file 'Wibbl' : No such file or directory
STACK Bio::Index::Abstract::open_dbm Bio/Index/Abstract.pm:398
STACK Bio::Index::Abstract::new Bio/Index/Abstract.pm:162
STACK Bio::Index::Blast::new Bio/Index/Blast.pm:143
STACK toplevel t/LocalDB/Index/Blast.t:20
-------------------------------------

# Looks like your test exited with 2 just after 3.
t/LocalDB/Index/Blast.t ................ 
Dubious, test returned 2 (wstat 512, 0x200)
Failed 23/26 subtests 
BDB1557 library build did not include support for cryptography
: No such file or directory

------------- EXCEPTION -------------
MSG: Can't open 'DB_File' dbm file 'Wibbl' : No such file or directory
STACK Bio::Index::Abstract::open_dbm Bio/Index/Abstract.pm:398
STACK Bio::Index::Abstract::new Bio/Index/Abstract.pm:162
STACK Bio::Index::BlastTable::new Bio/Index/BlastTable.pm:141
STACK toplevel t/LocalDB/Index/BlastTable.t:22
-------------------------------------

# Looks like your test exited with 2 just after 3.
t/LocalDB/Index/BlastTable.t ........... 
Dubious, test returned 2 (wstat 512, 0x200)
Failed 24/27 subtests 
BDB1557 library build did not include support for cryptography
: No such file or directory

------------- EXCEPTION -------------
MSG: Can't open 'DB_File' dbm file 'Wibbl' : No such file or directory
STACK Bio::Index::Abstract::open_dbm Bio/Index/Abstract.pm:398
STACK Bio::Index::Abstract::new Bio/Index/Abstract.pm:162
STACK Bio::Index::AbstractSeq::new Bio/Index/AbstractSeq.pm:93
STACK toplevel t/LocalDB/Index/Index.t:27
-------------------------------------

# Looks like your test exited with 2 just after 10.
t/LocalDB/Index/Index.t ................ 
Dubious, test returned 2 (wstat 512, 0x200)
Failed 63/73 subtests 
BDB1557 library build did not include support for cryptography
: No such file or directory

------------- EXCEPTION -------------
MSG: Could not open index file /tmp/S_u_Aa_yVq/dbqual/directory.index: No such file or directory
STACK Bio::DB::IndexedBase::_open_index Bio/DB/IndexedBase.pm:712
STACK Bio::DB::IndexedBase::_index_files Bio/DB/IndexedBase.pm:689
STACK Bio::DB::IndexedBase::index_dir Bio/DB/IndexedBase.pm:487
STACK Bio::DB::IndexedBase::new Bio/DB/IndexedBase.pm:402
STACK toplevel t/LocalDB/Qual.t:19
-------------------------------------

# Looks like your test exited with 2 just after 2.
t/LocalDB/Qual.t ....................... 
Dubious, test returned 2 (wstat 512, 0x200)
Failed 54/56 subtests 
BDB1557 library build did not include support for cryptography
: No such file or directory

------------- EXCEPTION -------------
MSG: Could not open primary index file: No such file or directory (did you remember to use -write_flag=>1?)
STACK Bio::DB::Flat::BDB::_open_bdb Bio/DB/Flat/BDB.pm:435
STACK Bio::DB::Flat::BDB::primary_db Bio/DB/Flat/BDB.pm:417
STACK Bio::DB::Flat::BDB::_store_primary Bio/DB/Flat/BDB.pm:352
STACK Bio::DB::Flat::BDB::_store_index Bio/DB/Flat/BDB.pm:338
STACK Bio::DB::Flat::BDB::_index_file Bio/DB/Flat/BDB.pm:249
STACK Bio::DB::Flat::BDB::build_index Bio/DB/Flat/BDB.pm:228
STACK toplevel t/LocalDB/Registry.t:42
-------------------------------------

# Looks like your test exited with 2 just after 4.
t/LocalDB/Registry.t ................... 
Dubious, test returned 2 (wstat 512, 0x200)
Failed 10/14 subtests 
BDB1557 library build did not include support for cryptography
: No such file or directory
BDB1557 library build did not include support for cryptography
: No such file or directory
BDB1557 library build did not include support for cryptography
: No such file or directory
BDB1557 library build did not include support for cryptography
: No such file or directory
Can't call method "seq" on an undefined value at Bio/DB/SeqFeature/Store/LoadHelper.pm line 173, <GEN0> line 1341.
# Looks like your test exited with 255 just after 36.
t/LocalDB/SeqFeature.t ................. 
Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 80/116 subtests 
t/LocalDB/Taxonomy/greengenes.t ........ ok
t/LocalDB/Taxonomy/silva.t ............. ok
t/LocalDB/Taxonomy/sqlite.t ............ skipped: The optional module DBD::SQLite (or dependencies thereof) was not installed
BDB1557 library build did not include support for cryptography
: No such file or directory

------------- EXCEPTION -------------
MSG: Cannot open file '/tmp/FOfpff7voo/nodes': No such file or directory
STACK Bio::DB::Taxonomy::flatfile::_build_index Bio/DB/Taxonomy/flatfile.pm:373
STACK Bio::DB::Taxonomy::flatfile::new Bio/DB/Taxonomy/flatfile.pm:141
STACK Bio::DB::Taxonomy::new Bio/DB/Taxonomy.pm:119
STACK toplevel t/LocalDB/transfac_pro.t:19
-------------------------------------

# Looks like your test exited with 2 just after 3.
t/LocalDB/transfac_pro.t ............... 
Dubious, test returned 2 (wstat 512, 0x200)
Failed 112/115 subtests 
t/Map/Cyto.t ........................... ok
t/Map/Linkage.t ........................ ok
t/Map/Map.t ............................ ok
t/Map/MapIO.t .......................... ok
t/Map/MicrosatelliteMarker.t ........... ok
t/Map/Physical.t ....................... ok
t/Matrix/IO/masta.t .................... ok
t/Matrix/IO/psm.t ...................... ok
t/Matrix/InstanceSite.t ................ ok
t/Matrix/Matrix.t ...................... ok
t/Matrix/ProtMatrix.t .................. ok
t/Matrix/ProtPsm.t ..................... ok
t/Matrix/SiteMatrix.t .................. ok
t/Ontology/GOterm.t .................... skipped: The optional module Graph::Directed (or dependencies thereof) was not installed
t/Ontology/GraphAdaptor.t .............. skipped: The optional module Graph (or dependencies thereof) was not installed
t/Ontology/IO/go.t ..................... skipped: The optional module Graph (or dependencies thereof) was not installed
t/Ontology/IO/interpro.t ............... skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed
t/Ontology/IO/obo.t .................... skipped: The optional module Graph (or dependencies thereof) was not installed
t/Ontology/Ontology.t .................. skipped: The optional module Graph (or dependencies thereof) was not installed
t/Ontology/OntologyEngine.t ............ skipped: The optional module Graph::Directed (or dependencies thereof) was not installed
t/Ontology/OntologyStore.t ............. skipped: The optional module Graph (or dependencies thereof) was not installed
t/Ontology/Relationship.t .............. skipped: The optional module Graph::Directed (or dependencies thereof) was not installed
t/Ontology/RelationshipType.t .......... skipped: The optional module Graph::Directed (or dependencies thereof) was not installed
t/Ontology/Term.t ...................... skipped: The optional module Graph::Directed (or dependencies thereof) was not installed
t/Perl.t ............................... ok
t/Phenotype/Correlate.t ................ ok
t/Phenotype/MeSH.t ..................... ok
t/Phenotype/Measure.t .................. ok
t/Phenotype/MiniMIMentry.t ............. ok
t/Phenotype/OMIMentry.t ................ ok
t/Phenotype/OMIMentryAllelicVariant.t .. ok
t/Phenotype/OMIMparser.t ............... ok
t/Phenotype/Phenotype.t ................ ok
t/PodSyntax.t .......................... skipped: Test::Pod 1.00 required for testing POD
t/PopGen/Coalescent.t .................. ok
t/PopGen/HtSNP.t ....................... ok
t/PopGen/MK.t .......................... ok
t/PopGen/PopGen.t ...................... ok
t/PopGen/PopGenSims.t .................. ok
t/PopGen/TagHaplotype.t ................ ok
t/RemoteDB/BioFetch.t .................. skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/CUTG.t ...................... skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/EMBL.t ...................... skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/EntrezGene.t ................ skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/GenBank.t ................... skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/GenPept.t ................... skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/HIV/HIV.t ................... skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/HIV/HIVAnnotProcessor.t ..... ok
t/RemoteDB/HIV/HIVQuery.t .............. skipped: The optional module CGI (or dependencies thereof) was not installed
t/RemoteDB/HIV/HIVQueryHelper.t ........ skipped: The optional module XML::Simple (or dependencies thereof) was not installed
t/RemoteDB/MeSH.t ...................... skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/Query/GenBank.t ............. skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/RefSeq.t .................... skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/SeqRead_fail.t .............. skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/SeqVersion.t ................ skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/SwissProt.t ................. skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/Taxonomy.t .................. skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/Restriction/Analysis-refac.t ......... ok
t/Restriction/Analysis.t ............... ok
t/Restriction/Gel.t .................... ok
t/Restriction/IO.t ..................... ok
t/Root/Exception.t ..................... ok
t/Root/HTTPget.t ....................... skipped: Network tests have not been requested
t/Root/IO.t ............................ ok
t/Root/RootI.t ......................... ok
t/Root/RootIO.t ........................ skipped: Network tests have not been requested
t/Root/Storable.t ...................... ok
t/Root/Utilities.t ..................... ok
t/SearchDist.t ......................... skipped: The optional module Bio::Ext::Align (or dependencies thereof) was not installed
t/SearchIO/CigarString.t ............... ok
t/SearchIO/SearchIO.t .................. ok
t/SearchIO/SimilarityPair.t ............ ok
t/SearchIO/Tiling.t .................... ok
t/SearchIO/Writer/GbrowseGFF.t ......... ok
t/SearchIO/Writer/HSPTableWriter.t ..... ok
t/SearchIO/Writer/HTMLWriter.t ......... ok
t/SearchIO/Writer/HitTableWriter.t ..... ok
t/SearchIO/Writer/TextWriter.t ......... ok
t/SearchIO/axt.t ....................... ok
t/SearchIO/blast.t ..................... ok
t/SearchIO/blast_pull.t ................ ok
t/SearchIO/blasttable.t ................ ok
t/SearchIO/cross_match.t ............... ok
t/SearchIO/erpin.t ..................... ok
t/SearchIO/exonerate.t ................. ok
t/SearchIO/fasta.t ..................... ok
t/SearchIO/gmap_f9.t ................... ok
t/SearchIO/hmmer.t ..................... ok
t/SearchIO/hmmer_pull.t ................ ok
t/SearchIO/infernal.t .................. ok
t/SearchIO/megablast.t ................. ok
t/SearchIO/psl.t ....................... ok
t/SearchIO/rnamotif.t .................. ok
t/SearchIO/sim4.t ...................... ok
t/SearchIO/waba.t ...................... ok
t/SearchIO/wise.t ...................... ok
t/Seq/DBLink.t ......................... ok
t/Seq/EncodedSeq.t ..................... ok
t/Seq/LargeLocatableSeq.t .............. ok
t/Seq/LargePSeq.t ...................... ok
t/Seq/LocatableSeq.t ................... ok
t/Seq/MetaSeq.t ........................ ok
t/Seq/PrimaryQual.t .................... ok
t/Seq/PrimarySeq.t ..................... ok
t/Seq/PrimedSeq.t ...................... ok
t/Seq/Quality.t ........................ ok
t/Seq/Seq.t ............................ ok
t/Seq/SimulatedRead.t .................. ok
t/Seq/WithQuality.t .................... ok
t/SeqEvolution.t ....................... ok
t/SeqFeature/Amplicon.t ................ ok
t/SeqFeature/Clone.t ................... ok
BDB1557 library build did not include support for cryptography
BDB0055 illegal flag specified to DB->set_ext_file_threshold
: No such file or directory

------------- EXCEPTION -------------
MSG: Unable to tie DB_File handle
STACK Bio::SeqFeature::Collection::new Bio/SeqFeature/Collection.pm:207
STACK toplevel t/SeqFeature/Collection.t:34
-------------------------------------

# Looks like your test exited with 2 just after 5.
t/SeqFeature/Collection.t .............. 
Dubious, test returned 2 (wstat 512, 0x200)
Failed 19/24 subtests 
t/SeqFeature/Computation.t ............. ok
t/SeqFeature/FeaturePair.t ............. ok
t/SeqFeature/Gene.t .................... ok
t/SeqFeature/Generic.t ................. ok
t/SeqFeature/Location.t ................ ok
t/SeqFeature/LocationFactory.t ......... ok
t/SeqFeature/Primer.t .................. ok
t/SeqFeature/Range.t ................... ok
t/SeqFeature/RangeI.t .................. ok
t/SeqFeature/SeqAnalysisParser.t ....... ok
t/SeqFeature/SubSeq.t .................. ok
t/SeqFeature/Unflattener.t ............. ok
t/SeqIO/Handler.t ...................... ok
t/SeqIO/MultiFile.t .................... ok
t/SeqIO/Multiple_fasta.t ............... ok
t/SeqIO/SeqBuilder.t ................... ok
t/SeqIO/SeqIO.t ........................ ok
t/SeqIO/Splicedseq.t ................... ok
t/SeqIO/abi.t .......................... skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
t/SeqIO/ace.t .......................... ok
t/SeqIO/agave.t ........................ skipped: The optional module XML::Writer (or dependencies thereof) was not installed
t/SeqIO/alf.t .......................... skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
t/SeqIO/asciitree.t .................... ok
t/SeqIO/bsml.t ......................... skipped: The optional module XML::DOM (or dependencies thereof) was not installed
t/SeqIO/bsml_sax.t ..................... skipped: The optional module XML::SAX::Writer (or dependencies thereof) was not installed
t/SeqIO/chadoxml.t ..................... skipped: The optional module XML::Writer (or dependencies thereof) was not installed
t/SeqIO/chaos.t ........................ ok
t/SeqIO/chaosxml.t ..................... ok
t/SeqIO/ctf.t .......................... skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
t/SeqIO/embl.t ......................... ok
t/SeqIO/entrezgene.t ................... skipped: The optional module Bio::ASN1::EntrezGene (or dependencies thereof) was not installed
t/SeqIO/excel.t ........................ skipped: The optional module Spreadsheet::ParseExcel (or dependencies thereof) was not installed
t/SeqIO/exp.t .......................... skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
t/SeqIO/fasta.t ........................ ok
t/SeqIO/fastq.t ........................ ok
t/SeqIO/flybase_chadoxml.t ............. skipped: The optional module XML::Writer (or dependencies thereof) was not installed
t/SeqIO/game.t ......................... skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed
t/SeqIO/gbxml.t ........................ ok
t/SeqIO/gcg.t .......................... ok
t/SeqIO/genbank.t ...................... ok
t/SeqIO/interpro.t ..................... skipped: The optional module XML::DOM::XPath (or dependencies thereof) was not installed
t/SeqIO/kegg.t ......................... ok
t/SeqIO/largefasta.t ................... ok
t/SeqIO/lasergene.t .................... ok
t/SeqIO/locuslink.t .................... skipped: The optional module Graph::Directed (or dependencies thereof) was not installed
t/SeqIO/mbsout.t ....................... ok
t/SeqIO/metafasta.t .................... ok
t/SeqIO/msout.t ........................ ok
t/SeqIO/nexml.t ........................ skipped: The optional module Bio::Phylo (or dependencies thereof) was not installed
t/SeqIO/phd.t .......................... ok
t/SeqIO/pir.t .......................... ok
t/SeqIO/pln.t .......................... skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
t/SeqIO/qual.t ......................... ok
t/SeqIO/raw.t .......................... ok
t/SeqIO/scf.t .......................... ok
t/SeqIO/seqxml.t ....................... skipped: The optional module XML::LibXML (or dependencies thereof) was not installed
t/SeqIO/strider.t ...................... skipped: The optional module Convert::Binary::C (or dependencies thereof) was not installed
t/SeqIO/swiss.t ........................ ok
t/SeqIO/tab.t .......................... ok
t/SeqIO/table.t ........................ skipped: The optional module IO::Scalar (or dependencies thereof) was not installed
t/SeqIO/tigr.t ......................... skipped: The optional module Error (or dependencies thereof) was not installed
t/SeqIO/tigrxml.t ...................... skipped: The optional module XML::SAX::Writer (or dependencies thereof) was not installed
t/SeqIO/tinyseq.t ...................... skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed
t/SeqIO/ztr.t .......................... skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
t/SeqTools/Backtranslate.t ............. ok
t/SeqTools/CodonTable.t ................ ok
t/SeqTools/ECnumber.t .................. ok
t/SeqTools/GuessSeqFormat.t ............ ok
t/SeqTools/OddCodes.t .................. ok
t/SeqTools/SeqPattern.t ................ ok
t/SeqTools/SeqStats.t .................. ok
t/SeqTools/SeqUtils.t .................. ok
t/SeqTools/SeqWords.t .................. ok
t/Species.t ............................ ok
t/Structure/IO.t ....................... ok
t/Structure/Structure.t ................ ok
t/Symbol.t ............................. ok
t/TaxonTree.t .......................... skipped: These modules are now probably deprecated
t/Tools/Alignment/Consed.t ............. ok
t/Tools/AmpliconSearch.t ............... ok
t/Tools/Analysis/DNA/ESEfinder.t ....... skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/Tools/Analysis/Protein/Domcut.t ...... skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/Tools/Analysis/Protein/ELM.t ......... skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/Tools/Analysis/Protein/GOR4.t ........ skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/Tools/Analysis/Protein/HNN.t ......... skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/Tools/Analysis/Protein/NetPhos.t ..... skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/Tools/Analysis/Protein/Scansite.t .... skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/Tools/Analysis/Protein/Sopma.t ....... skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/Tools/EMBOSS/Palindrome.t ............ ok
t/Tools/Est2Genome.t ................... ok
t/Tools/FootPrinter.t .................. ok
t/Tools/GFF.t .......................... ok
t/Tools/Geneid.t ....................... ok
t/Tools/Genewise.t ..................... ok
t/Tools/Genomewise.t ................... ok
t/Tools/Genpred.t ...................... ok
t/Tools/Hmmer.t ........................ ok
t/Tools/IUPAC.t ........................ ok
t/Tools/Lucy.t ......................... ok
t/Tools/Match.t ........................ ok
t/Tools/Phylo/Gerp.t ................... ok
t/Tools/Phylo/Molphy.t ................. ok
t/Tools/Phylo/PAML.t ................... ok
t/Tools/Phylo/Phylip/ProtDist.t ........ ok
t/Tools/Primer3.t ...................... ok
t/Tools/Promoterwise.t ................. ok
t/Tools/Pseudowise.t ................... ok
t/Tools/QRNA.t ......................... ok
t/Tools/RandDistFunctions.t ............ ok
t/Tools/RepeatMasker.t ................. ok
t/Tools/Run/RemoteBlast.t .............. skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/Tools/Run/RemoteBlast_rpsblast.t ..... skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/Tools/Seg.t .......................... ok
t/Tools/SiRNA.t ........................ ok
t/Tools/Sigcleave.t .................... ok
t/Tools/Signalp.t ...................... ok
t/Tools/Signalp/ExtendedSignalp.t ...... ok
t/Tools/Sim4.t ......................... ok
t/Tools/Spidey/Spidey.t ................ ok
t/Tools/TandemRepeatsFinder.t .......... ok
t/Tools/TargetP.t ...................... ok
t/Tools/Tmhmm.t ........................ ok
t/Tools/ePCR.t ......................... ok
t/Tools/pICalculator.t ................. ok
t/Tools/tRNAscanSE.t ................... ok
t/Tree/Compatible.t .................... skipped: The optional module Set::Scalar (or dependencies thereof) was not installed
t/Tree/Node.t .......................... ok
t/Tree/PhyloNetwork/Factory.t .......... skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed
t/Tree/PhyloNetwork/GraphViz.t ......... skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed
t/Tree/PhyloNetwork/MuVector.t ......... ok
t/Tree/PhyloNetwork/PhyloNetwork.t ..... skipped: The optional module Graph::Directed (or dependencies thereof) was not installed
t/Tree/PhyloNetwork/RandomFactory.t .... skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed
t/Tree/PhyloNetwork/TreeFactory.t ...... skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed
t/Tree/RandomTreeFactory.t ............. ok
t/Tree/Tree.t .......................... ok
t/Tree/TreeIO.t ........................ ok
t/Tree/TreeIO/lintree.t ................ ok
t/Tree/TreeIO/newick.t ................. ok
t/Tree/TreeIO/nexml.t .................. skipped: The optional module Bio::Phylo (or dependencies thereof) was not installed
t/Tree/TreeIO/nexus.t .................. ok
t/Tree/TreeIO/nhx.t .................... ok
t/Tree/TreeIO/phyloxml.t ............... skipped: The optional module XML::LibXML (or dependencies thereof) was not installed
t/Tree/TreeIO/svggraph.t ............... ok
t/Tree/TreeIO/tabtree.t ................ ok
t/Tree/TreeStatistics.t ................ ok
t/Variation/AAChange.t ................. ok
t/Variation/AAReverseMutate.t .......... ok
t/Variation/Allele.t ................... ok
t/Variation/DNAMutation.t .............. ok
t/Variation/RNAChange.t ................ ok
t/Variation/SNP.t ...................... ok
t/Variation/SeqDiff.t .................. ok
t/Variation/Variation_IO.t ............. skipped: The optional module XML::Writer (or dependencies thereof) was not installed
t/nexml.t .............................. skipped: The optional module Bio::Phylo (or dependencies thereof) was not installed

Test Summary Report
-------------------
t/LocalDB/Fasta.t                    (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 109 tests but ran 0.
t/LocalDB/Flat.t                     (Wstat: 512 Tests: 2 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 25 tests but ran 2.
t/LocalDB/Index/Blast.t              (Wstat: 512 Tests: 3 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 26 tests but ran 3.
t/LocalDB/Index/BlastTable.t         (Wstat: 512 Tests: 3 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 27 tests but ran 3.
t/LocalDB/Index/Index.t              (Wstat: 512 Tests: 10 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 73 tests but ran 10.
t/LocalDB/Qual.t                     (Wstat: 512 Tests: 2 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 56 tests but ran 2.
t/LocalDB/Registry.t                 (Wstat: 512 Tests: 4 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 14 tests but ran 4.
t/LocalDB/SeqFeature.t               (Wstat: 65280 Tests: 36 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 116 tests but ran 36.
t/LocalDB/transfac_pro.t             (Wstat: 512 Tests: 3 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 115 tests but ran 3.
t/SeqFeature/Collection.t            (Wstat: 512 Tests: 5 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 24 tests but ran 5.
Files=325, Tests=17866, 133 wallclock secs ( 4.47 usr  3.61 sys + 110.58 cusr 17.87 csys = 136.53 CPU)
Result: FAIL
Failed 10/325 test programs. 0/17866 subtests failed.
-> FAIL Installing Bio::Root::Version failed. See /home/linuxbrew/.cpanm/work/1502408933.12319/build.log for details. Retry with --force to force install it.

SLURM job scheduler

The most commonly used job scheduler with Singularity or bioinformatics analysis jobs is Slurm. Here are its benefits:

load balancing between multiple nodes
limiting ram/process job size
limiting job time

Implementation -- singularity_job.slurm

#!/bin/bash 
#SBATCH --ntasks=1     # number of tasks/processes run in this job 
#SBATCH --time=01:00:00     # one hour runtime limit 
#SBATCH --mem-per-cpu=4096   # default is 1GB, max memory required per CPU
#SBATCH --nodes=2
#SBATCH --output=slurm.out
#SBATCH --cpus-per-task=1
#SBATCH --requeue  # if allocated node hangs, job requeued 
#SBATCH --gres=lscratch:500  # max scratch disk space available for use in /lscratch, in GB   -- when job is terminated, all data in /lscratch/$SLURM_JOB_ID directory will be automatically deleted (if data needs to be saved, copy to /data before job concludes 

CONTAINER=/opt/singularity/orca.simg
OVERLAY=/$HOME/.orca/overlay.simg

module load singularity
# hostname
singularity build ${CONTAINER} ${OVERLAY}    # run program/command on resource allocated

Submit the job

$ sbatch singularity_job.slurm
$ cat slurm-<jobid>.out
$ squeue

Etc

mkdir lscratch
export SINGULARITY_BINDPATH="/data/$USER:/data,/fdb:/resources,/lscratch/$SLURM_JOB_ID:/tmp"
singularity shell my-container.simg

"we use symbolic links to refer to our network storage systems. As a result, you will need to bind some additional directories to the ones you know of and use directly to ensure that the symbolic link destinations are also bound into the container." hpc nih

Changing TMPDIR from /tmp (8GB per node) to /lscratch (set your own limit)

this also is better for multi user accesses
allocate local scratch disk for jobs

#!/bin/bash
export TMPDIR=/lscratch/$SLURM_JOB_ID

brew install ... doesn't work (Martin's class)

Temporary solution:

First create this directory:

mkdir -p -m775 ~/.cache/Homebrew

Then create a .bashrc (dot bashrc) file in their home directory. To do this, you can copy the code between the dotted line. And paste into the terminal:

echo '# .bashrc
 
# Source global definitions
if [ -f /etc/bashrc ]; then
        . /etc/bashrc
fi
 
# Uncomment the following line if you don't like systemctl's auto-paging feature:
# export SYSTEMD_PAGER=
 
# User specific aliases and functions
alias brew='sudo -u linuxbrew HOMEBREW_NO_AUTO_UPDATE=1 /home/linuxbrew/.linuxbrew/bin/brew'
' >> ~/.bashrc

Then log out and log back in for it to take effect.

Now brew install nano will work for example

Possible permanent solution for future (Hackseq?):

mount the file .bashrc in read-only mode ( docker run -v ....:ro )
run container in the backround mode (docker run -d ...)
execute a container and pass the command mkdir -p -m775 ~/.cache/Homebrew (
docker exec -it -u $(id -u):$(id -g) <<<CONTAINER_ID>>> /bin/bash -c "mkdir -p -m775 ~/.cache/Homebrew && /bin/bash”)

Have to be fixed before 2017.08 release

brew install fails:
(The list is based on the high priority list)

delly (https://github.com/Homebrew/homebrew-science/pull/5412)
discovardenovo (#19)
gubbins (Homebrew/homebrew-science#5752)
masurca (Homebrew/homebrew-science#5772)
mira (#20)
pbsuite (https://github.com/Homebrew/homebrew-science/pull/5685 + conflict, bedtools: because Both install bin/bamToFastq)
poretools (#21)

brew test fails:

blasr blasr: revision for hdf5 https://github.com/Homebrew/homebrew-science/pull/5688

brew linkage --test fails:

blasr #3
lobstr https://github.com/Homebrew/homebrew-science/pull/5861
[email protected] #15

brew cite

Create a brew cite foo command that returns an URL (or optionally Bibtex) for the requested tool and its dependencies.

Usage

❯❯❯ brew cite samtools
http://doi.org/10.1093/bioinformatics/btp352
❯❯❯ brew cite --bib samtools
@article{Li_2009, title={The Sequence Alignment/Map format and SAMtools}, volume={25}, ISSN={1460-2059}, url={http://dx.doi.org/10.1093/bioinformatics/btp352}, DOI={10.1093/bioinformatics/btp352}, number={16}, journal={Bioinformatics}, publisher={Oxford University Press (OUP)}, author={Li, H. and Handsaker, B. and Wysoker, A. and Fennell, T. and Ruan, J. and Homer, N. and Marth, G. and Abecasis, G. and Durbin, R.}, year={2009}, month={Jun}, pages={2078–2079}}

Options

-b or --bib return Bibtex entries rather than an URLs
-1 return only the requested formulae and not their dependencies

Implementation

The code and data lives in a GitHub repository linuxbrew/homebrew-cite.
The data will be stored in a TSV file in the same repository with two columns, Formula and Citation.

The --bib option uses the doi.org service to fetch the Bibtex entry. For example:

curl -LH "Accept: text/bibliography; style=bibtex" http://dx.doi.org/10.1093/bioinformatics/btp352

An example of a similar command is the old brew desc command that was eventually migrated into Homebrew/brew. https://github.com/telemachus/homebrew-desc/blob/master/cmd/brew-desc.rb

Install cwltool

Please install cwltool like so

pip install cwlref-runner

See https://github.com/common-workflow-language/cwltool#install
Thanks!

htseq: error: too many arguments to function

    pysam/libchtslib.c: In function '__Pyx_PyCFunction_FastCall':
    pysam/libchtslib.c:15077:12: error: too many arguments to function '(PyObject * (*)(PyObject *, PyObject * const*, Py_ssize_t))meth'
         return (*((__Pyx_PyCFunctionFast)meth)) (self, args, nargs, NULL);

https://hub.docker.com/r/bcgsc/orca-1/builds/brdtjmj5vdtd9ifucknylnu/

@suujia Can you see if you can find any reference to this error on the upstream GitHub repo?
https://github.com/simon-anders/htseq

Create a formula for singularity

Please create a formula for Singularity and submit it to https://github.com/Linuxbrew/homebrew-extra
http://singularity.lbl.gov/quickstart

brew create --tap=linuxbrew/extra https://github.com/singularityware/singularity/releases/download/2.3.1/singularity-2.3.1.tar.gz

Create a Brewfile for ORCA

See https://github.com/Homebrew/homebrew-bundle

Singularity:Overview

For Singularity version: 2.4.1

Singularity Recipe:
https://github.com/bcgsc/orca/blob/master/Singularity.1

Build the image MANUALLY:

sudo singularity build orca.simg Singularity1

Each user should create an overlay:

singularity image.create --size 3000 overlay.simg 
singularity shell --overlay overlay.simg orca.simg

Problem: During the building image MANUALLY the following error appears: Cannot mkdir: No space left on device during building
Explanation: /tmp/ is full
Solution: Change cash and tmp directory using environment variables.
SINGULARITY_CACHEDIR for persistent things, and SINGULARITY_TMPDIR for temporary things during build.

For example:

SINGULARITY_DISABLE_CACHE=Yes
export SINGULARITY_DISABLE_CACHE
SINGULARITY_CACHEDIR=/home/tmozgacheva/tmp/tmp
export SINGULARITY_CACHEDIR
SINGULARITY_TMPDIR=/home/tmozgacheva/tmp
export SINGULARITY_TMPDIR

AUTOMATED build in Singularity hub (https://singularity-hub.org/) :

Better to set up the manual trigger:
singularityhub/singularityhub.github.io#95

Current issue is not solved:
singularityhub/singularityhub.github.io#94

Change bash to bash -l

Running bash reads only ~/.bashrc. Running bash -l also reads ~/.profile.
Please change /bin/bash to /bin/bash -l here:
https://github.com/bcgsc/orca/blob/master/scripts/orca#L29
and here:
https://github.com/bcgsc/orca/blob/master/scripts/orca#L34

discovardenovo

==> Installing homebrew/science/discovardenovo
==> Downloading ftp://ftp.broadinstitute.org/pub/crd/DiscovarDeNovo/latest_source_code/discovardenovo-52488.tar.gz
######################################################################## 100.0%
==> ./configure --disable-silent-rules --prefix=/home/linuxbrew/.linuxbrew/Cellar/discovardenovo/52488
==> make install
Last 15 lines from /home/linuxbrew/.cache/Homebrew/Logs/discovardenovo/02.make:
make[1]: *** [CrossOut] Error 1
make[1]: *** Waiting for unfinished jobs....
libDiscovarDeNovo.a(GapToyCore.o): In function `GapToyCore(int, char**)':
/tmp/discovardenovo-20170816-914-1loskbi/discovardenovo-52488/src/paths/long/large/GapToyCore.cc:625: undefined reference to `digraphE<BaseVec>::O(int) const'
libDiscovarDeNovo.a(FinalFiles.o): In function `FinalFiles(HyperBasevector const&, vec<int, std::allocator<int> > const&, MasterVec<ReadPath> const&, vec<FeudalString<char, std::char_traits<char> >, std::allocator<FeudalString<char, std::char_traits<char> > > > const&, vec<long, std::allocator<long> > const&, FeudalString<char, std::char_traits<char> > const&, FeudalString<char, std::char_traits<char> > const&, int, int, unsigned char, FeudalString<char, std::char_traits<char> > const&, unsigned char const&, FeudalString<char, std::char_traits<char> > const&, std::map<FeudalString<char, std::char_traits<char> >, GapToyResults, std::less<FeudalString<char, std::char_traits<char> > >, std::allocator<std::pair<FeudalString<char, std::char_traits<char> > const, GapToyResults> > >&, FeudalString<char, std::char_traits<char> > const&, FeudalString<char, std::char_traits<char> > const&, vec<int, std::allocator<int> > const&, MasterVec<BaseVec> const&, unsigned char)':
/tmp/discovardenovo-20170816-914-1loskbi/discovardenovo-52488/src/paths/long/large/FinalFiles.cc:249: undefined reference to `digraphE<BaseVec>::O(int) const'
libDiscovarDeNovo.a(Improve60.o): In function `Improve60(HyperBasevector&, vec<int, std::allocator<int> >&, MasterVec<ReadPath>&, MasterVec<BaseVec> const&, MasterVec<PQVecA<MempoolAllocator<unsigned char> > > const&, unsigned char) [clone ._omp_fn.0]':
/tmp/discovardenovo-20170816-914-1loskbi/discovardenovo-52488/src/paths/long/large/Improve60.cc:92: undefined reference to `digraphE<BaseVec>::O(int) const'
/tmp/discovardenovo-20170816-914-1loskbi/discovardenovo-52488/src/paths/long/large/Improve60.cc:94: undefined reference to `digraphE<BaseVec>::O(int) const'
/tmp/discovardenovo-20170816-914-1loskbi/discovardenovo-52488/src/paths/long/large/Improve60.cc:68: undefined reference to `digraphE<BaseVec>::O(int) const'
libDiscovarDeNovo.a(Improve60.o):/tmp/discovardenovo-20170816-914-1loskbi/discovardenovo-52488/src/paths/long/large/Improve60.cc:68: more undefined references to `digraphE<BaseVec>::O(int) const' follow
collect2: error: ld returned 1 exit status
make[1]: *** [DiscovarDeNovo] Error 1
make[1]: Leaving directory `/tmp/discovardenovo-20170816-914-1loskbi/discovardenovo-52488/src'
make: *** [install-recursive] Error 1

mira: exp_flexer.cc

==> Installing homebrew/science/mira
==> Downloading https://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira-4.0.2.tar.bz2
==> Downloading from https://superb-dca2.dl.sourceforge.net/project/mira-assembler/MIRA/stable/mira-4.0.2.tar.bz2
######################################################################## 100.0%
==> ./configure --prefix=/home/linuxbrew/.linuxbrew/Cellar/mira/4.0.2 --with-expat=/home/linuxbrew/.linuxbrew/opt/expat --with-expat-lib=-L/home/linuxbrew/.linuxbrew/opt/exp
==> make LIBS='-lboost_regex-mt -lboost_system-mt -lboost_filesystem-mt -lboost_iostreams-mt -lboost_thread-mt -lexpat -lz'
Last 15 lines from /home/linuxbrew/.cache/Homebrew/Logs/mira/02.make:
In file included from exp_flexer.cc:323:0:
/home/linuxbrew/.linuxbrew/include/FlexLexer.h:156:8: error: candidate is: void EXPFlexLexer::yy_init_buffer(yy_buffer_state*, std::istream&)
   void yy_init_buffer( yy_buffer_state* b, std::istream& s );
        ^
make[5]: *** [exp_flexer.o] Error 1
make[5]: Leaving directory `/tmp/mira-20170816-8616-4nd1wo/mira-4.0.2/src/io'
make[4]: *** [all] Error 2
make[4]: Leaving directory `/tmp/mira-20170816-8616-4nd1wo/mira-4.0.2/src/io'
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory `/tmp/mira-20170816-8616-4nd1wo/mira-4.0.2/src'
make[2]: *** [all] Error 2
make[2]: Leaving directory `/tmp/mira-20170816-8616-4nd1wo/mira-4.0.2/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/tmp/mira-20170816-8616-4nd1wo/mira-4.0.2'
make: *** [all] Error 2

READ THIS: https://github.com/Linuxbrew/brew/blob/master/docs/Troubleshooting.md#troubleshooting
Please do not report this issue to Homebrew/brew or Homebrew/core, which support macOS only.

These open issues may also help:
mira: Add desc and rename google-perftools https://github.com/Homebrew/homebrew-science/pull/5522
mira: exp_flexer.cc:766:9: error: no match for 'operator=' https://github.com/Homebrew/homebrew-science/issues/3424
mira error quirks.C:56:5: error: 'cout' is not a member of 'std' https://github.com/Homebrew/homebrew-science/issues/2268

Install for HackSeq image

Singularity build

shub:bcgsc/orca
shub:suujia/orca

Not sure how to trigger a rebuild for the bcgsc/orca shub. The error message I got with a build on suujia/orca shub was:

+ su -c brew install perl -v linuxbrew
Error: /home/linuxbrew/.linuxbrew/Homebrew is not writable. You should change the
ownership and permissions of /home/linuxbrew/.linuxbrew/Homebrew back to your
user account:
sudo chown -R $(whoami) /home/linuxbrew/.linuxbrew/Homebrew
Error: Cannot write to /home/linuxbrew/.linuxbrew
ABORT: Aborting with RETVAL=255

I think I'll start with getting it to build locally first and updating singularity file to align with orca dockerfile.

Correct message: ~/Software/bin

Please change ~/Software/bin to /home/linuxbrew/.linuxbrew/bin
https://github.com/bcgsc/orca/blob/master/scripts/orca#L21

Write Documentation

How to set up Docker, Docker Swarm, create accounts etc.

Tag a stable release of ORCA

Singularity: linubrew folder disappers with --writable flag

Problem: usually a singularity container is read-only (brew install, apt-get don't work).
In order to edit a container, --writable flag is used. However, the brew command disappeared (see a sample script below) because linuxbrew folder doesn't exist in the folder /home!

singularity pull docker://tmozgacheva/orca:latest
singularity shell orca-latest.mg

Singularity orca-latest.img:~/sing> which brew
/home/linuxbrew/.linuxbrew/bin/brew

exit

singularity shell --writable orca-latest.mg
Singularity orca-latest.img:~/sing> which brew
Singularity orca-latest.img:~/sing> 
Singularity orca-latest.img:~/sing> brew --version
bash: brew: command not found

Question: could we adapt the singularity for our purpose because we need a function that edits a container !?

Add unicycler

I created a new formula for Unicycler. Please add it to the ORCA image.
https://github.com/Homebrew/homebrew-science/pull/6146

Build dockerfile with Quay

https://quay.io/repository/suujia/orca/build/89d6336c-b862-4b64-864d-0f50086b7f42

I combined orca into one dockerfile and built it on Quay. Needs debugging.

Address failed tests

See https://cloud.docker.com/u/bcgsc/repository/registry-1.docker.io/bcgsc/orca/builds/1800f55e-41da-4adb-930a-aaedbc6d6322

Table of GitHub metadata and analytics

Hi, Tanya. Can you please prepare a table that lists…

the number of GitHub watchers, stars, and forks for each formula in Homebrew/science that has a GitHub a repo https://github.com/Linuxbrew/brew/blob/master/Library/Homebrew/dev-cmd/audit.rb#L592-L604
whether the formula is notable (forks ≥ 20 or watchers ≥ 20 or stars ≥ 50)
the number of macOS installations in the last year https://brew.sh/analytics/install/
the number of Linuxbrew installations in the last year (/home/tmozgacheva/science-20170914.csv)
whether the formula has a # tag "bioinformatics"

Fix broken brew test

Add TSV file of installed formula and their versions

Please commit to this repo the TSV file used to generate https://tmozgach.github.io/orca/
Just the list of current version. The previous versions aren't needed.

Add hub to the ORCA image

brew install hub

Migrate containers

Problem: how to migrate a running container from one worker to another worker.
Flocker:?
https://github.com/ClusterHQ/flocker

Add missing brewsci/bio formulae to ORCA

abricate
bali-phy
bandage
berokka
bonsai
cannoli
circos
consel
elph
ema
emboss
exabayes
fastp
finch-rs
flye
genome-painter
gfalint
k8
kent-tools
kma
lastz
magic-blast
mosdepth
mp-est
mpboot
nextflow
orfm
phyx
porechop
portcullis
prank
quickmerge
quicktree
r8s
rapidnj
raxml-ng
realphy
rtg-tools
samclip
seq-gen
seqkit
tigmint
transdecoder
treepl
uniqtag
varsim

Fix failed tests

See https://hub.docker.com/r/bcgsc/orca/builds/bkugb8zp2colunaf5ngggya/

bowtie: Can't locate Clone.pm
mlst: Can't locate List/MoreUtils.pm
prokka: Can't locate Bio/Root/Version.pm
simulate-pcr: Can't locate Bio/SeqIO.pm
trinity: execution expired
unzip: Failed executing: /usr/bin/zip
velvetoptimiser: Can't locate Bio/SeqIO.pm

See https://hub.docker.com/r/bcgsc/orca/builds/b2wrhgjdp4ijkxvns7z8zr/

bamm: Enable multithreading to use std::thread: Operation not permitted

$ bamm -c divcontrol.txt
BAMM 2.5.0 (2015-11-01)
Copyright (C) 2012-2014 Daniel Rabosky
BAMM is distributed under the GNU General Public License.
See http://bamm-project.org for more information.

Random seed: 1496970488

…

Running 4 chains for 10000 generations.

terminate called after throwing an instance of 'std::system_error'
  what():  Enable multithreading to use std::thread: Operation not permitted
Aborted (core dumped)

Fix broken brew linkage --test

Determine license

Formulae fail after updating boost, linuxbrew

Install:

sga works in empty image =>something influences on it

Test:

circlator https://github.com/Homebrew/homebrew-science/pull/6216
discovar https://github.com/Homebrew/homebrew-science/pull/6275 => RUN brew install [email protected] solves
express => RUN brew install [email protected] solves
kat RUN brew install [email protected] solves
mapsembler2 RUN brew install [email protected] solves
mummer works in empty image =>something influences on it

/home/linuxbrew/.linuxbrew/Cellar/mummer/3.23_2/mummerplot -h 2>&1
Error: homebrew/science/mummer: failed
</U(sage|SAGE)/> expected to be =~
<"Can't use 'defined(%hash)' (Maybe you should just omit the defined()?) at /home/linuxbrew/.linuxbrew/Cellar/mummer/3.23_2/mummerplot line 884.\n">.

poretools works in empty image =>something influences on it

==> /home/linuxbrew/.linuxbrew/Cellar/poretools/0.6.0_6/libexec/bin/pip install -v --no-deps --no-binary :all: --ignore-installed /tmp/poretools--h5py-20170901-18
Last 15 lines from /home/linuxbrew/.cache/Homebrew/Logs/poretools/06.pip:
  Removing source in /tmp/pip-C409WA-build
Command "/home/linuxbrew/.linuxbrew/Cellar/poretools/0.6.0_6/libexec/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-C409WA-build/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-hdaw0X-record/install-record.txt --single-version-externally-managed --compile --install-headers /home/linuxbrew/.linuxbrew/Cellar/poretools/0.6.0_6/libexec/include/site/python2.7/h5py" failed with error code 1 in /tmp/pip-C409WA-build/
Exception information:
Traceback (most recent call last):
  File "/home/linuxbrew/.linuxbrew/lib/python2.7/site-packages/pip/basecommand.py", line 215, in main
    status = self.run(options, args)
  File "/home/linuxbrew/.linuxbrew/lib/python2.7/site-packages/pip/commands/install.py", line 342, in run
    prefix=options.prefix_path,
  File "/home/linuxbrew/.linuxbrew/lib/python2.7/site-packages/pip/req/req_set.py", line 784, in install
    **kwargs
  File "/home/linuxbrew/.linuxbrew/lib/python2.7/site-packages/pip/req/req_install.py", line 878, in install
    spinner=spinner,
  File "/home/linuxbrew/.linuxbrew/lib/python2.7/site-packages/pip/utils/__init__.py", line 707, in call_subprocess
    % (command_desc, proc.returncode, cwd))
InstallationError: Command "/home/linuxbrew/.linuxbrew/Cellar/poretools/0.6.0_6/libexec/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-C409WA-build/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-hdaw0X-record/install-record.txt --single-version-externally-managed --compile --install-headers /home/linuxbrew/.linuxbrew/Cellar/poretools/0.6.0_6/libexec/include/site/python2.7/h5py" failed with error code 1 in /tmp/pip-C409WA-build/

repeatmasker
sdsl-lite brew test sdsl-lite --cc=gcc-4.9

Broken Tools

abricate
XS.c: loadable library and perl binaries are mismatched (got handshake key 0xde00080, needed 0xce00080) The post-install step did not complete successfully�
atram
contains conflicting version recursive dependencies: isl, [email protected], gcc@6, gcc (error: fails on linuxbrew/linuxbrew image as well as dockerhub)
bandage
dependency on pulseaudio, which is broken shown in PR: [pulseaudio: Build a bottle for Linuxbrew](https://github.com/Linuxbrew/homebrew-core/pull/8429)
phylip

The `brew link` step did not complete successfully�
The formula built, but is not symlinked into /home/linuxbrew/.linuxbrew
Could not symlink bin/consense
Target /home/linuxbrew/.linuxbrew/bin/consense
is a symlink belonging to exabayes. You can unlink it:
  brew unlink exabayes

trimal
dependency: express

warning: 'LOG_MAX' defined but not used [-Wunused-variable]
 const double LOG_MAX = log(std::numeric_limits<double>::max());
make[1]: Leaving directory '/tmp/express-20180803-15658-19ihh8h/express-1.5.1-src'
Makefile:132: recipe for target 'all' failed
express: migrate to brewsci/bio https://github.com/brewsci/homebrew-science/pull/188

trinity
dependency: express

same issue as above, broken dependency
when installed on docker image:

brewsci/science/trinity contains conflicting version recursive dependencies:
  isl, [email protected], gcc@6, gcc

Fix brew linkage --test [email protected]

brew linkage --test [email protected]
shows the following

System libraries:
  /lib/x86_64-linux-gnu/libc.so.6
  /lib/x86_64-linux-gnu/libdl.so.2
  /lib/x86_64-linux-gnu/libpthread.so.0
Missing libraries:
  libcrypto.so.1.1
  libssl.so.1.1

and

/lib/x86_64-linux-gnu/libc.so.6
  bin/openssl
  lib/engines-1.1/capi.so
  lib/engines-1.1/padlock.so
  lib/libcrypto.so.1.1
  lib/libssl.so.1.1

/lib/x86_64-linux-gnu/libdl.so.2
  lib/libcrypto.so.1.1

/lib/x86_64-linux-gnu/libpthread.so.0
  bin/openssl
  lib/engines-1.1/capi.so
  lib/engines-1.1/padlock.so
  lib/libcrypto.so.1.1
  lib/libssl.so.1.1

libcrypto.so.1.1
  bin/openssl
  lib/engines-1.1/padlock.so
  lib/libssl.so.1.1

libssl.so.1.1
  bin/openssl

BioBuilds vs ORCA (Missing software)

ORCA paper

Title:?
Format: Application note (2 pages)
Deadline:?
Journals:

Bioinformatics provides a forum for the exchange of information in the fields of computational molecular biology and post-genome bioinformatics, with emphasis on the documentation of new algorithms and databases that allows the progress of bioinformatics and biomedical research in a significant manner. (https://academic.oup.com/bioinformatics)
Bioinformatics and Biology Insights The journal welcomes all submissions in the field of bioinformatics and also submissions dealing with the relationship between bioinformatics and the broader field of biology. Submissions of original research, reviews, tutorials, rapid communications, expert commentaries, letters, application notes, and point–counter-point articles are welcomed for peer review. (http://insights.sagepub.com/journal.php?pa=aims_and_scope&journal_id=39)
BMC Bioinformatics is an open access, peer-reviewed journal that considers articles on all aspects of the development, testing and novel application of computational and statistical methods for the modeling and analysis of all kinds of biological data, as well as other areas of computational biology. (https://bmcbioinformatics.biomedcentral.com/about)
OUP Database is platform for the presentation of novel ideas in database research surrounding biological information, and aims to help strengthen the bridge between database developers, curators, and users. (https://academic.oup.com/database/pages/About)
Briefings in Bioinformatics The journal publishes reviews for the users of databases and analytical tools of contemporary genetics, molecular and systems biology and is unique in providing practical help and guidance to the non-specialist in computerized methodology. (https://academic.oup.com/bib/pages/About)
Computational and Structural Biotechnology Journal The journal places a strong emphasis on functional and mechanistic understanding of how molecular components in a biological process work together through the application of computational methods. The journal welcomes the submission of manuscripts that meet the general criteria of significance and scientific excellence, and enables the rapid publication of papers under the following categories:
Research articles
Review articles
Mini Reviews
Highlights
Communications
Software/Web server articles
(https://www.journals.elsevier.com/computational-and-structural-biotechnology-journal)
EMBNET.JOURNAL The main focus of EMBnet.journal is on the latest developments in bioinformatics research, in tools and resources, in training and education, and in standards and best practice. (https://www.embnet.org/wp/)
GigaScience As an open access and open-data journal, we publish ALL research objects (data, software tools and workflows) from 'big data' studies across the entire spectrum of life and biomedical sciences. (https://academic.oup.com/gigascience)
eLife publishes important research in all areas of the life and biomedical sciences. (https://elifesciences.org/about)
Structure:

Add jupyter to the ORCA image

Here's my PR to bottle it.
Homebrew/linuxbrew-core#4600

For future

biopieces (export variables automatically, example, vcftools {xxx: ,yyy:})
zip (create formulae)
CWL
a container: delete or exit function

Run dockerfilelint using TravisCI

See for example https://github.com/Linuxbrew/docker/pull/15/files

Fix broken formulae

The Bold forlmulae is a forlmulae that exists in the old ORCA and absents in the new ORCA (brew list)

Libraries:

Failed Tests

Run GUI apps in a container

Example: igv
Dockerfile:

FROM linuxbrew/linuxbrew
ENV PERL5LIB /home/linuxbrew/perl5/lib/perl5
RUN sudo apt-get update && sudo apt-get install -y \
	software-properties-common \
	default-jre \
	wget \
	unzip \
	glib-networking-common
RUN brew tap homebrew/science
RUN brew install igv
USER 1992

How do I run graphical programs remotely from a Linux server for different OS:
https://uisapp2.iu.edu/confluence-prd/pages/viewpage.action?pageId=280461906

Singularity: appropriate workaround?

@sjackman could you please look into my solution to that problem and tell me, could we do that?
Or may be you have a more elegant suggestion.

Given: an immutable container with linuxbrew, only nano installed by brew
What we would like to get: install permanently for example, 'vim', inside the container.
My solution:
Dockerfile (tmozgacheva/orca-a):

FROM linuxbrew/linuxbrew 
RUN brew install nano
USER root
RUN chmod -R 777 /home/linuxbrew/.linuxbrew

sudo singularity build linuxbrewt3.simg docker://tmozgacheva/orca-a 
singularity image.create --size 3000 overlay.simg 
singularity shell --overlay overlay.simg linuxbrewt3.simg

The problem: We can not run brew as linuxbrew user using sudo -u linuxbrew brew as we did it before for Hackseq! When I add the following line %orca_users ALL=(linuxbrew) NOPASSWD:ALL in sudoers, inside the container, I get the following error when I run brew:

sudo: effective uid is not 0, is /usr/bin/sudo on a file system with the 'nosuid' option set or an NFS file system without root privileges?

And we can not to do anything, singularity prevents run command as sudo.
Only one way that I see, it is to make /home/linuxbrew/.linuxbrew folder writable for everyone! (e,g, RUN chmod -R 777 /home/linuxbrew/.linuxbrew)
However, I am in doubt that it is good solution but in that way, it work!
What do you think about it?

Packages cannot be bottled cause they have Perl/Python package dependency

Revise README.md

Please remove Removed packages and instead link to https://bcgsc.github.io/orca/
Please move https://tmozgach.github.io/orca/ to https://bcgsc.github.io/orca/

bcgsc / orca Goto Github PK

orca's Introduction

ORCA

Genomics Research Container Architecture

Contributing

orca's People

Contributors

Stargazers

Watchers

Forkers

orca's Issues

Implementation -- singularity_job.slurm

Submit the job

Etc

Changing TMPDIR from /tmp (8GB per node) to /lscratch (set your own limit)

Usage

Options

Implementation

Recommend Projects

Recommend Topics

Recommend Org