Comments (5)
VDJer relies upon Google's sparsehash may have issues on Mac. If you're open to experimenting, you could try replacing the sparsehash currently used in VDJer with Google's latest version: https://github.com/sparsehash/sparsehash/
I'll try to find a Mac on which to test here, but cannot promise a quick turnaround.
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Thanks, I'll try to install the GitHub version of sparsehash. If you think it is because of the Mac, I will also switch to Linux and have a go.
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If you have access to a Linux machine, I'd recommend going that route. All of our runs have been on Linux.
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I've followed your advice and updated the sparsehash. A new error now appeared:
src/main/c/vj_filter.c:312:2: error: use of undeclared identifier 'pthread_mutex_init'
pthread_mutex_init(&vjf_mutex, NULL);
^
On a more positive note, it indeed compiled without issue on a linux machine, so I'll use that for the time being.
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Fyi I got this same issue when running the 0.92-SNAPSHOT-with-dependencies jar
src/main/c/sparsehash/sparse_hash_map:94:10: fatal error: 'tr1/functional' file not found
I first installed the g++ compiler for mac (Sierra) through macports:
https://www.macports.org/install.php
Then ran the make file after changing this:
native: mktargetdir
g++ -g -I$(SRCDIR) -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux -shared -fPIC $(SRCDIR)/assembler.c -o target/libAbra.so
To this:
native: mktargetdir
/opt/local/bin/g++-mp-4.7 -g -I$(SRCDIR) -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux -shared -fPIC $(SRCDIR)/assembler.c -o target/libAbra.so
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Related Issues (17)
- segmentation fault (core dumped) HOT 3
- Mouse references and indices HOT 5
- --ins parameter HOT 1
- Does VDJer work on BAMs from HISAT2? HOT 4
- Unexpected output from v'djer HOT 3
- Post processing light chains HOT 4
- "Initial char in input invalid" HOT 5
- Few alignments output HOT 2
- Absent IGH contigs HOT 7
- VDJER extracts no clones on bam file produced with STAR HOT 2
- Extracting useful reads HOT 2
- STAR 1-pass vs 2-pass HOT 2
- Core dump while running bam files HOT 1
- VDJer: empty output HOT 5
- problem running vdjer on bam file from GTEx HOT 6
- can vdjer work on whole-exome sequencing data? HOT 5
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