Question: How to install samtools from shed_tool on local galaxy
0
gravatar for biowz
3.4 years ago by
biowz0
United States
biowz0 wrote:

Hi, would you like to show my detailed information to install samtools on local galaxy. The step on manual online I followed finally failed

 

 

 

galaxy samtools • 1.9k views
ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by biowz0

Can you provide us with the error message. Thanks!

ADD REPLYlink written 3.4 years ago by Bjoern Gruening5.1k
0
gravatar for biowz
3.4 years ago by
biowz0
United States
biowz0 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. 

ADD COMMENTlink written 3.4 years ago by biowz0

Which Galaxy version are you using? Can you try to have < 1.0 samtools on your $PATH?

ADD REPLYlink written 3.4 years ago by Bjoern Gruening5.1k
0
gravatar for biowz
3.4 years ago by
biowz0
United States
biowz0 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 

ADD COMMENTlink written 3.4 years ago by biowz0
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