Question: How to install samtools from shed_tool on local galaxy
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biowz • 0 wrote:
when I used HISAT software, I met this error as follow:
Dataset 33: HISAT on data 3Tool execution generated the following error message:
Fatal error: Exit code 1 ()
Usage: samtools sort [options...] [in.bam]
Options:
-l INT Set compression level, from 0 (uncompressed) to 9 (best)
-m INT Set maximum memory per thread; suffix K/M/G recognized [768M]
-n Sort by read name
-o FILE Write final output to FILE rather than standard output
-O FORMAT Write output as FORMAT ('sam'/'bam'/'cram') (either -O or
-T PREFIX Write temporary files to PREFIX.nnnn.bam -T is required)
-@ INT Set number of sorting and compression threads [1]
Legacy usage: samtools sort [options...] <in.bam> <out.prefix>
Options:
-f Use <out.prefix> as full final filename rather than prefix
-o Write final output to stdout rather than <out.prefix>.bam
-l,m,n,@ Similar to corresponding options above
samtools: writing to standard output failed: Broken pipe
samtools: error closing standard output: -1
Error while flushing and closing output
libc++abi.dylib: terminating with uncaught exception of type int
(ERR): hisat-align died with signal 6 (ABRT)
[bam_header_read] bgzf_check_EOF: Invalid argument
Galaxy attempted to build the BAM index with samtools 1.0+ but failed: [Errno 2] No such file or directory: '/Users/biowzmailustceducn/galaxy/database/job_working_directory/000/40/__dataset_43_metadata_temp_file_b5rEcP.bai'
This may means I do not install samtools, thus I download samtools and put this .zip file into tool_shed and install this tool through terminal command.
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biowz • 0 wrote:
I do not know the version of galaxy, I just follow instruction to install galaxy. Can you tell me how to check the version? I will download <1.0 samtools to install in tool-shed. I do not know how to add this into my $path which galaxy software can recognize. Thank you very much !
Best Regards
Zheng
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Can you provide us with the error message. Thanks!