Question: Error when install tool from galaxy tool shed
gravatar for GPS
4.5 years ago by
GPS20 wrote:

Hello Everyone

I upload my softsearch tool in to galaxy tool shed for that I create two repositories first repository contain 

the file tool_dependencies.xml, softsearch.xml and tool-data directory 

tool_dependencies.xml file contains:

<?xml version="1.0"?>
    <package name="softsearch" version="1.0.0">
        <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 this repository contain another tool_dependencies.xml file 

tool_dependencies.xml file contain:

<?xml version="1.0"?>
    <package name="softsearch" version="2.4">
        <repository toolshed="" name="ss-tool" owner="plus" changeset_revision="962d5485ca5e" />



changeset_revision="962d5485ca5e" on above file is revision id of first repository was created

but when I install this repositories in my local galaxy instance it will show the error

Name Version Type Status Error
softsearch 1.0.0 package Error Can't locate in @INC (@INC contains: /data2/bsi/reference/softsearch/lib /etc/perl /usr/local/lib/perl/5.14.2 /usr/local/share/perl/5.14.2 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.14 /usr/share/perl/5.14 /usr/local/lib/site_perl .) at script/ line 16. BEGIN failed--compilation aborted at script/ line 16.

so please any one can tell me how solved this error and tell me I am doing correct or wrong


Thank You


ADD COMMENTlink modified 4.5 years ago by Dave B.410 • written 4.5 years ago by GPS20
gravatar for fubar
4.5 years ago by
fubar1.1k wrote:

I don't have a solution but a few seconds with google search revealed which seems to suggest that the problem exists in Galaxy-free environments and so probably has more to do with the package itself, the vagaries of your local perl installation and the specific source code you are working with.

It also seems to me that running as the galaxy user during the installation is unlikely to work for your system perl which is owned by root and which should refuse to allow non-superusers to (eg) install CPAN modules - if that's what is trying to do. Please take a close look at the tool installation log which will probably show that the Galaxy user had insufficient rights to install from CPAN. If that hunch is true, you may need to add a package_perl dependency and make sure that the Galaxy user is running against the perl installation owned by the Galaxy user to make the kinds of changes needs to make so the softsearch perl script can run. 

I'm sure this will be very useful to others so thanks for working on this.  

ADD COMMENTlink written 4.5 years ago by fubar1.1k
gravatar for Jennifer Hillman Jackson
4.5 years ago by
United States
Jennifer Hillman Jackson25k wrote:


I found multiple repositories named for this tool in the main tool shed and some in the test tool shed, sometimes under slightly different author names (perhaps an error upon upload?). While you are working out the process, using the test tool shed is probably a good idea (this is intended to be a sandbox for learning purposes). Also, if you examine your repositories versus others on the main tool shed, you will be able to see how they differ in metadata and contents, along with warning messages about how all dependencies must be in the same tool shed. Do this in conjunction with reviewing the tool shed instructions (not all problems will have detailed warnings):

To get started, please see the tool shed documentation here:

There is also a very comprehensive tutorial for creating repositories here:

It was not clear if the tool and wrapper were functioning before upload as a repository, along with test data (from prior posts), but that would be important. The links above explain the dependencies and contents for a valid repository.

Best, Jen, Galaxy team

ADD COMMENTlink modified 4.5 years ago • written 4.5 years ago by Jennifer Hillman Jackson25k
gravatar for GPS
4.5 years ago by
GPS20 wrote:

Hello Jennifer 

Thanks for reply . I following all the link and read the documentation and as per documentation I upload my tool on galaxy test tool shed ( but when I install  tool into local galaxy instance i will get the error on installation status .

Monitor installing tool shed repositories

Name Description Owner Revision Status
ss_test_tool SoftSearch is Sensitive Structural Varient detection(SV) tool plus91 00b9898b8510




and when i click in ss_test_tool it will show error message

This repository is not installed correctly (see the Repository installation error below). Choose Reset to install from the Repository Actions menu, correct problems if necessary and try installing the repository again.


when i try to clone the repository by the command prompt it will show  the error.


abort: error: _ssl.c:504: error:14090086:SSL routines:SSL3_GET_SERVER_CERTIFICATE:certificate verify failed



can u please tell me solution...


Thank You




ADD COMMENTlink modified 4.5 years ago • written 4.5 years ago by GPS20
gravatar for y.hoogstrate
4.5 years ago by
y.hoogstrate460 wrote:


I'm experiencing the same error. What I've noticed is that if you browse to:

You will be redirected to


So my guess is that the testtoolshed has changed to HTTPS.

This would not be a very big issue at itself. However, if you use e.g. "wget" to download from the testtoolshed:


wget crashes with a certificate error:


--2014-06-04 15:29:42--
Connecting to||:443... connected.
ERROR: cannot verify's certificate, issued by ‘/C=US/O=Internet2/OU=InCommon/CN=InCommon Server CA’:
  Unable to locally verify the issuer's authority.
To connect to insecurely, use `--no-check-certificate'.


For some reason my browser (chromium) accepts this certificate, but WGET and PYTHON do not... I hope this will be solved soon, since updating en installing from the testtoolshed are not working anymore.



ADD COMMENTlink written 4.5 years ago by y.hoogstrate460

you can use the  --no-check-certificate switch to make wget ignore cert errors

ADD REPLYlink written 4.5 years ago by Martin Čech ♦♦ 4.9k

I use this to explain that there's something 'wrong' with the SSL certificate. The command you give solves only the wget problem (in a way you can argue about...).

Galaxy can not install tools from the test toolshed because the python SSL wrappers give certificate errors as well, just as wget does. As GPS already mentioned:

 error:14090086:SSL routines:SSL3_GET_SERVER_CERTIFICATE:certificate verify failed

This stops further installation of any tool in the test tool shed (since the test tool shed requires a SSL connection using HTTP redirect).

I also tested it on a clean install of galaxy, and this problem is still there.

ADD REPLYlink modified 4.5 years ago • written 4.5 years ago by y.hoogstrate460

Please try again and let us know if this is still not working for you. Thanks.

ADD REPLYlink written 4.5 years ago by Daniel Blankenberg ♦♦ 1.7k

The issue has been fixed on my computer(s). I can not reproduce it anymore. Thanks!!


However, installation of tools from the testtoolshed still keeps crashing because of the HTTP -> HTTPS redirection.

I solved this by changing the URL of the testtoolshed to in the "tool_sheds_conf.xml".

ADD REPLYlink modified 4.5 years ago • written 4.5 years ago by y.hoogstrate460

Hii all 

Thanks for replying me. I successfully upload my tool into galaxy tools shed but after I install the tool from tool shed to local galaxy  instance it will display a message of successfully installed but cant execute the tool_dependency file store in tool dependency type repository the tool dependency file i already post so please tell me the tool_dependency file is correct or not

After successfully installing the tool it will create installation.log and file 

installation.log file contain installation of softsearch tool

and file contain the path like

PATH=/home/data/galaxy-dist/tool_dependency_dir/vdt/0.6/priti/vdt_dependency/44abb6a5a98f/bin:$PATH; export PATH


any one can tell me solution on this


Thank You


ADD REPLYlink written 4.5 years ago by GPS20
gravatar for Dave B.
4.5 years ago by
Dave B.410
United States
Dave B.410 wrote:

The error in loading the module may be due to the prefix specified when running For better results, I suggest replacing $PWD with $INSTALL_DIR in the tool_dependencies.xml

The reason for this is that the tool dependency installation process creates a temporary directory for building the package, which is deleted after the build process finishes. During this process, $PWD is set to the path of that temporary directory, rather than the directory where the built package will be installed. The tool dependency installation process replaces the variable $INSTALL_DIR with the installation directory of the finished package.

ADD COMMENTlink written 4.5 years ago by Dave B.410

Hii Dave

Thanks for reply me and its working and  install binaries in galaxy tool dependency directory path set in to universe_wsgi.ini file  (tool_dependency_dir = /home/data/galaxy-dist/tool_dependency_dir) but i want to pass this to my xml wrapper file so that it can be search file and execute the tool into galaxy.

(<command>#if $source.index_source=="history" 
            samtools index $bam_file ; samtools faidx $source.history_fasta_file ; $inc | perl -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 | perl -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        


so please can any one tell me solution on this..


Thank You


ADD REPLYlink written 4.5 years ago by GPS20
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