NONCODE is a database of all kinds of noncoding RNAs (except tRNAs and rRNAs)

http://www.noncode.org/download.php

http://wash.github.io/rnacode/

galaxytools should be restructured to look and feel like the tools-iuc and tools-devteam repository.

To reflect the different areas of tools and to keep the links stable I will have different tools directories.

• rna-tools
• chemicaltoolbox

Remove useless script from the root and improve the readme file.

Got this error trying to implement MACS2 callpeak...this doesn't happen with MACS1.4:

Traceback (most recent call last):
File "/local/cluster/bin/macs2", line 362, in
main()
File "/local/cluster/bin/macs2", line 45, in main
run( args )
File "/local/cluster/lib/python2.7/site-packages/MACS2/callpeak.py", line 55, in run
options = opt_validate( args )
File "/local/cluster/lib/python2.7/site-packages/MACS2/OptValidator.py", line 184, in opt_validate
if options.refine_peaks:
AttributeError: 'Namespace' object has no attribute 'refine_peaks'
Full Command: macs2 callpeak -t aGFP_align_sorted.bam -c input_align_sorted.bam -f BAM -g 245000000 -p 1.00e-5 -n aGFP --verbose 3

We can do a lot better in structuring and writing documentations for our tools:

• bismark wrapper
• statistical hypothesis testing

@erasche a thought a little bit more about it and I think we should remove the FASTA output completely and offer a tool which extracts the correct sequences from the input fasta + the gff file. So what we need is one wrapper that extracts sequences from a FASTA file given a corresponding gff/gtf/BED file.

whole genome association analysis toolset
https://www.cog-genomics.org/plink2

Does aragorn_out_to_gff3.py handle introns? It doesn't appear to after scanning the code. Feature request? Here's an example of a few tRNA with introns.

3   tRNA-Val              c[883351,883869]  35      (tac)i(40,443)
5   tRNA-seC               [244644,244785]  87      (tca)i(29,57)
7   tRNA-Arg               [615338,616255]  36      (tcg)i(40,822)
2   tRNA-Ser               [324667,326116]  35      (gga)i(40,1354)
1   tRNA-Val                c[84563,87002]  2383    (tac)i(34,2347)
1   tRNA-Asp              c[114384,114687]  39      (atc)i(43,206)
4   tRNA-seC               [324290,324369]  36      (tca)i(38,6)
5   tRNA-Ser               [345441,345776]  28      (gct)i(33,251)
7   tRNA-Val               [405066,405293]  34      (cac)i(35,133)
3   tRNA-Asn               [367853,369971]  2062    (att)i(32,2028)
3   tRNA-Pro               [234486,236430]  1887    (agg)i(31,1856)
1   tRNA-Ser                 [66020,66741]  32      (gct)i(37,633)
2   tRNA-Leu                 [84137,84224]  36      (tag)i(38,10)
3   tRNA-Arg               [168865,170209]  1285    (gcg)i(32,1253)
4   tRNA-His               [175766,176602]  776     (gtg)i(34,742)
1   tRNA-seC                c[88201,88280]  36      (tca)i(38,6)

Presently prinseq/tool_dependencies.xml downloads and installs bowtie2 v2.1.0, which may be provided instead by devteam's package_bowtie2_2_1_0 in the Tool Shed.
This just came to my eyes while looking at this file, I've not tested the possible change.

compalignp

Tool for comparison of alignments

It's picking up my tabular test dataset (pasted entries with spaces OR spaces converted to tabs)

Add argument to tool parameters. See here: galaxyproject/galaxy#8

My colleague Paolo Uva noticed that the gatk2_unified_genotyper tool creates a number of threads which is 6 times the number of cores it has been assigned in job_conf.xml (i.e. $GALAXY_SLOTS). This is due to the options "--num_threads ${GALAXY_SLOTS:-4}" (specified by the macro @threads@) and "--num_cpu_threads_per_data_thread 6".

When this job runs on a machine where it is supposed to occupy only a part of the available CPU cores, it harms the performances of other jobs.

The easiest solution is obviously to change the second option to "--num_cpu_threads_per_data_thread 1".

Jmol is capatized as Jmol and not JMol.

Option --interval_padding, which is accepted by all GATK tools, is missing.

The param is a non-negative integer, default is 0. Help text should be "Amount of padding (in bp) to add to each interval" .

It should be added to standard_gatk_options and gatk_param_type_conditional macro.

Metagenomic species profiling using universal phylogenetic marker genes.

http://www.bork.embl.de/software/mOTU/download.html

This seems to be like a nice alternative to get galaxy in docker preinstalled and test tools with planemo.
Since we have the information from tool_dependencies.xml we could even install packages from the TS before testing tools.

https://www.shippable.com/

@erasche I would appreciate your opinion as expert in this field!

orphan_tool_dependencies/package_blat_35x1/tool_dependencies.xml contains:

<url_template os="linux" architecture="x86_64">https://github.com/bgruening/download_store/raw/master/ucsc/linux/x86_64/blat_35x1</url_template>
<url_template os="darwin" architecture="i686">https://github.com/bgruening/download_store/raw/master/ucsc/darwin/i386/blat_35x1</url_template>
<url_template os="darwin" architecture="i386">https://github.com/bgruening/download_store/raw/master/ucsc/darwin/i386/blat_35x1</url_template>
<url_template os="darwin" architecture="x86_64">https://github.com/bgruening/download_store/raw/master/ucsc/darwin/x86_64/blat_35x1</url_template>

but since bgruening/download_store@bea3c95 all these files have been removed.

Would be happy if that tool could be integrated :-)

http://omictools.com/targetfinder-s7192.html

The documentation of the tool specifies 10 output columns. 11 are actually produced, columns 2 & 3 should be combined

Unix tools is now known as text-processing tools. We need to add some tests and add missing tools.

• tool tests
• missing tools ?
• send Assaf Gordon a beer for his initial wrappers

On L18 of msa/datatypes_conf.xml, the sniffer is listed as

<sniffer type="galaxy.datatypes.infernal:Stockholm_1_0"/>

whilst the actual datatype is listed as

<datatype extension="stockholm" type="galaxy.datatypes.msa:Stockholm_1_0" display_in_upload="True" />

Should galaxy.datatypes.infernal be galaxy.datatypes.msa?

The sailfish wrapper is work in progress.

• loc file handling
• data manager
• check parameter
• add unit-test

Moreover it will be replaced by Salmon, some github repository.

xref: https://github.com/bgruening/galaxytools/tree/master/tools/sailfish

http://www.jcheminf.com/content/7/1/35

The idea is to collect as many annotations as possible and put then into a data store, like sqlite. Answering questions and querying should be separate tools on-top of this storage. Pretty much like gemini.

This library seems to be well maintained: https://github.com/daler/gffutils

Use the new $__tool_directory__ feature and replace the old SCRIPT_PATH variables.

https://bitbucket.org/galaxy/galaxy-central/commits/ddbe0d12bc86da406bb96213e23b8ddb273ed669#comment-1610704

• augustus
• bismark
• crt
• deseq2
• diffbind
• glimmer_w_icm
• convert_graph
• interproscan
• MiClip
• minced
• prinseq
• inforna
• trna_prediction
• exparna
• text_processing (grep, easyjoin)

Tracking bug report for missing tools test.

• suspenders
• blockbuster
• diffbind
• ChemicalToolBox

Process a coordinate-sorted and indexed BAM or CRAM file containing some form of BS-seq alignments and extract per-base methylation metrics from them

https://github.com/dpryan79/PileOMeth

We have a few nice infernal wrappers but a few tools are still missing.

We should finish up the HOMER tool suite.

@peterjc @erasche (because your are both heavily involved in genome annotation).
We are running a genome annotation workshop in the end of this month here and I would like to include our biopython tools from: https://github.com/bgruening/galaxytools/tree/master/tools/biopython into the TS before. I started this many years back but never put them into the TS.

I'm planning to add

• tests
• tool dependencies
• citations
• macros

What is your opinion on one biopython tool repository vs. many single repositories?
Should I put everything in one github folder but trying the planemo demultiplexing feature to create several TS repositories?
Are these tools good enough?
Should I skip a few (e.g. translate?), because they are already in EMBOSS?
General comments?

Hi Bjoern,
since Prokka requires Aragorn, it would be useful if you can create a new package_aragorn_1_2_36 repository containing the relevant part from trna_prediction/tool_dependencies.xml .

TIA

http://smithlabresearch.org/software/piranha/

We need this for your RNA workshop in one month.

Brain cell finder is a tool for fully automated localization of soma in 3D mouse brain images acquired by confocal light sheet microscopy.

https://github.com/paolo-f/bcfind

Started here:
https://github.com/bgruening/galaxytools/blob/master/tools/image_processing/bcfind/bcfind.xml

• NIPY community packages, http://nipy.org/ Set of software tools supporting Brain Imaging Data Structure (BIDS) standard, http://bids.neuroimaging.io/
• QAP (quality assesment), http://preprocessed-connectomes-project.org/quality-assessment-protocol/
• MRIQC (quality assessment), http://mriqc.readthedocs.io/en/stable/
• FMRIPREP (preprocessing workflow), https://github.com/poldracklab/fmriprep
• Automatic Analysis (fMRI processing toolbox), https://github.com/rhodricusack/automaticanalysis
• OpenfMRI2BIDS BIDS2ISATab, DCM2NIIx, DICM2NII, BIDSto3col, BIDS2NDA, AFNI BIDS-tools, heudiconv, Dcm2Bids, bidskit, dac2bids (format converters)
• OpenfMRI (repository), https://openfmri.org/
• C-PAC (Configurable Pipeline for the Analysing Connectomes), http://fcp-indi.github.io/
• Brainstorm (MEG/EEG analysis package), http://neuroimage.usc.edu/brainstorm/ Set of tools supported within BrainSuite, http://brainsuite.org/
• Tensorflow, https://www.tensorflow.org/
  Useful for brain segmentation and detection, classification tasks

For example, which CDK version are you using? Alternatively, add a pointer in the README where this information can be found elsewhere, e.g. in the repository.

The GotohScan program is a search tool that finds shorter sequences
(usually genes) in large database sequences (chromosomes, genomes, ..)
by computing all semi-global alignments. Thus, the query sequence is
never truncated or split into subsequences, but always mapped to the
database over its complete length. The alignment is computed via the
Gotoh-alignment algorithm using affine gap costs.

http://www.bioinf.uni-leipzig.de/Software/GotohScan/

Wrapper update needed: http://bioinf.uni-greifswald.de/augustus/binaries/

Predicting the interaction between long noncoding RNAs and proteins. By coding RNA and protein sequences into vectors, we use matrix multiplication to give score to each RNA-protein pair. This score can be the measurement of interactions between the RNA-protein pair.

http://bioinfo.bjmu.edu.cn/lncpro/
Requested by Gregor Klaus via mail.

https://www.bioinf.uni-leipzig.de/Software/proteinortho/

Needs to be integrated. + We have a VIS for this http://www.vicbioinformatics.com/software.fripan.shtml

@TorHou we now have rna_eps as datatype in galaxy-central.
https://bitbucket.org/galaxy/galaxy-central/commits/dd67f14145f75cbbe9ab3e73d40088a669139f07

Would be great to use it in all our RNA tools.

Seqway: https://www.pmgenomics.ca/hoffmanlab/proj/segway/
https://bitbucket.org/hoffmanlab/segway/overview

(ChromHMM: http://compbio.mit.edu/ChromHMM/)

PEAR - http://www.exelixis-lab.org/pear
FLASh - http://ccb.jhu.edu/software/FLASH/

preferring PEAR?

@bgruening You mentioned you started wrappers for PEAR...

https://github.com/mourisl/Lighter

AntiSmash3 was released and we should update our wrapper.
blocking: https://bitbucket.org/antismash/antismash/pull-request/1/make-structure-drawer-cluster-aware/diff#comment-7367945

samblaster is a fast and flexible program for marking duplicates in read-id grouped1 paired-end SAM files. It can also optionally output discordant read pairs and/or split read mappings to separate SAM files, and/or unmapped/clipped reads to a separate FASTQ file. When marking duplicates, samblaster will require approximately 20MB of memory per 1M read pairs.

https://github.com/GregoryFaust/samblaster

http://bejerano.stanford.edu/great/public/html/
Many coding genes are well annotated with their biological functions. Non-coding regions typically lack such annotation. GREAT assigns biological meaning to a set of non-coding genomic regions by analyzing the annotations of the nearby genes. Thus, it is particularly useful in studying cis functions of sets of non-coding genomic regions

Tbl2asn is a command-line program that automates the creation of sequence records for submission to GenBank. It uses many of the same functions as Sequin but is driven generally by data files. Tbl2asn generates .sqn files for submission to GenBank. Additional manual editing is not required before submission.

http://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/

http://mafft.cbrc.jp/alignment/software/

MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc.

This exists already -> https://toolshed.g2.bx.psu.edu/view/basfplant/mafft/e4d26cd8be10, but will need to be conformed - also needs a tool_dependencies.xml

I see this error:
bam_tview_curses.c:5:20: error: curses.h: No such file or directory bam_tview_curses.c:7:2: warning: #warning "_CURSES_LIB=1 but NCURSES_VERSION not defined; tview is NOT compiled" bam_tview_curses.c:287:2: warning: #warning "No curses library is available; tview with curses is disabled." make[1]: *** [bam_tview_curses.o] Error 1 make: *** [all-recur] Error 1

no curses library (or ncurses)...

I can build manually if i set D_CURSES_LIB=0 and comment -lcurses