Question: How to install samtools from shed_tool on local galaxy
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  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.
Which Galaxy version are you using? Can you try to have < 1.0 samtools on your $PATH?
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 !
Can you provide us with the error message. Thanks!