Tool: error when upload tool in tool shed.
gravatar for Shirish
4.5 years ago by
Shirish20 wrote:

Hi all,


I integrate the SoftSearch tool in local galaxy successfully. Then I upload my tool in galaxy tool shed on this link But when I install it on another local galaxy system I face the problem of path.

/bin/sh: 1: /home/plus91/shed_tools/ not found

It happened due to parent repository(e3609c8714fb) always generate new by galaxy tool shed so please tell me how i can fix the repository path and name of repository.

For that I wrote a xml like this..


<?xml version="1.0"?>

<tool id="SoftSearch" name="SoftSearch">
  <description>for structure variation</description>
  <command>#if $source.index_source=="history" 
            samtools index $bam_file ; samtools faidx $source.history_fasta_file ; $inc | ~/shed_tools/ -l $min_length_soft_clip -q $min_map_quality -r $min_depth_soft_clip_loc -m $min_no_discordant_read -s $no_sd_consider_discordant -b $bam_file -f $source.history_fasta_file -o $out_file1
        samtools index $bam_file ; samtools faidx $source.ref_fasta.fields.path ; $inc | ~/shed_tools/ -l $min_length_soft_clip -q $min_map_quality -r $min_depth_soft_clip_loc -m $min_no_discordant_read -s $no_sd_consider_discordant -b $bam_file -f $source.ref_fasta.fields.path -o $out_file1
        #end if        
      <param name="bam_file" type="data"   format="bam" label="BAM Files" />
     <conditional name="source">
            <param name="index_source" type="select" label="Choose the source for the reference list">
                <option value="cached">Locally cached</option>
                <option value="history">History</option>
            <when value="history">
                <param format="fasta" name="history_fasta_file" type="data" label="Fasta file from history."/>
            <when value="cached">
                  <param name="ref_fasta" type="select" >
                    <options from_data_table="fasta_indexes">
                    <validator type="no_options" message="No Fasta file is available" />
      <param name="inc" type="hidden" value="n=$RANDOM" />
         <param name="min_length_soft_clip" type="integer" value="10" label="-l Minimum length of soft-clipped segment [5]" /> 
        <param name="min_map_quality" type="integer" value="20" label="-q Minimum mapping quality [20]" />     
    <param name="min_depth_soft_clip_loc" type="integer" value="10" label="-r Minimum depth of soft-clipped reads at position [5]" /> 
    <param name="min_no_discordant_read" type="integer" value="10" label="-m Minimum number of discordant read pairs [5]" /> 
    <param name="no_sd_consider_discordant" type="integer" value="4" label="-s Number of sd away from mean to be considered discordant" />       
      <data format="vcf" name="out_file1" />


So please can anyone tell me which directory and files are necessary for uploading tool into tool shed and please tell me process of uploading tool into tool shed.










tool software error galaxy • 1.4k views
ADD COMMENTlink modified 4.5 years ago by Bjoern Gruening5.1k • written 4.5 years ago by Shirish20
gravatar for Bjoern Gruening
4.5 years ago by
Bjoern Gruening5.1k
Bjoern Gruening5.1k wrote:

Hi Shirish,

you should never never use paths in your wrapper. If is a single file, just include it next to your wrapper. If it needs to be installed, write a tool_dependencies.xml file, as described here and related pages. Galaxy and the Tool Shed will take care about the path and the libraries if you do it correct and in the end you only need to call without a path at the beginning.

Please use the to test your tool until it is ready. We would like to reduce broken packages from main toolshed.



ADD COMMENTlink written 4.5 years ago by Bjoern Gruening5.1k

Hi Bjoern, 

As you said I followed all step. First I create one repository called "ss_tool" on " " then I upload "softesearch" directory on that, in which too_dependencies.xml, softsearch.xml and tool-data directory. 

tool_dependencies.xml file contains:


<?xml version="1.0"?>
    <package name="softsearch" version="0.6">
        <install version="1.0">
        <action type="download_by_url">
        <action type="shell_command">perl ./ --prefix=$PWD</action>
                <action type="shell_command">export PERL5LIB=$PERL5LIB:$PWD:$PWD/lib</action>
        <action type="shell_command">perl script/</action>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>


Then I create another repository called "complex_repository_dependencies_on_softsearch". in which I upload one another tool_dependencies.xml file. It contains:


<?xml version="1.0"?>
    <package name="softsearch" version="0.6">
        <repository toolshed="" name="ss_tool" owner="shirish" changeset_revision="6292bd3c9ffa" />


After that I check it on my local system, It will create only those file which I uploaded on

and It provide error like this...


Name Version Type Status Error
softsearch 0.6 package Error

File "/home/plus91/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/", line 289, in install_and_build_package_via_fabric tool_dependency = fabric_util.install_and_build_package( app, tool_dependency, actions_dict ) File "/home/plus91/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/", line 357, in install_and_build_package dir = td_common_util.url_download( work_dir, downloaded_filename, url, extract=True ) File "/home/plus91/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/", line 452, in url_download chunk = suc.CHUNK_SIZE ) File "/usr/lib/python2.7/", line 380, in read data = self._sock.recv(left) File "/usr/lib/python2.7/", line 561, in read s = File "/usr/lib/python2.7/", line 380, in read data = self._sock.recv(left) File "/usr/lib/python2.7/", line 241, in recv return File "/usr/lib/python2.7/", line 160, in read return [Errno 104] Connection reset by peer


can you tell me why this happened.?



ADD REPLYlink written 4.5 years ago by Shirish20
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