Hello, I'm following "Managed Tool Dependencies" to the letter and still can't get Galaxy to find the executable. Is this page https://wiki.galaxyproject.org/Admin/Config/ToolDependencies up to date? If yes, what am I doing wrong? Any help greatly appreciated! # universe_wsgi.ini # I also tried the absolute path, it made no difference tool_dependency_dir = tool_dependencies # tool_dependencies is set like instructed: $ ls tool_dependencies/hhsuite/ 2.0.16/ default@ $ ls tool_dependencies/hhsuite/2.0.16/bin ffindex_build* ffindex_get* hhalign* hhblits* hhconsensus* hhfilter* hhmake* hhsearch* My tool: <tool id="hhpred_hhblits_01" name="Create MSA from single fasta for hhsearch" hidden="false" version="1.0.0" force_history_refresh="true"> <requirement type="package">hhsuite</requirement> <description>Searches single fasta iteratively against hmm db to build a MSA</description> <command>hhblits -i $input_file -d $database -oa3m $outfile</command> etc... Galaxy throws Error: hhblits not found. I've tried setting the PATH in the tool_dependencies/hhsuite/2.0.16/env.sh: #!/bin/bash # configure PATH to hhsuite binaries PATH="/opt/galaxy-dist/tool_dependencies/hhsuite/default/bin:$PATH" export PATH still getting hhblits not found :-( What am I doing wrong? Isabelle
Hi, can you try: <requirements> <requirement type="package">hhsuite</requirement> </requirements> Hope that helps, sorry for the short answer I'm too tired :) Bjoern Am 31.05.2014 01:53, schrieb Isabelle Phan:
Hello,
I'm following "Managed Tool Dependencies" to the letter and still can't get Galaxy to find the executable. Is this page https://wiki.galaxyproject.org/Admin/Config/ToolDependencies up to date? If yes, what am I doing wrong?
Any help greatly appreciated!
# universe_wsgi.ini # I also tried the absolute path, it made no difference tool_dependency_dir = tool_dependencies
# tool_dependencies is set like instructed:
$ ls tool_dependencies/hhsuite/ 2.0.16/ default@ $ ls tool_dependencies/hhsuite/2.0.16/bin
ffindex_build* ffindex_get* hhalign* hhblits* hhconsensus* hhfilter* hhmake* hhsearch*
My tool: <tool id="hhpred_hhblits_01" name="Create MSA from single fasta for hhsearch" hidden="false" version="1.0.0" force_history_refresh="true"> <requirement type="package">hhsuite</requirement> <description>Searches single fasta iteratively against hmm db to build a MSA</description> <command>hhblits -i $input_file -d $database -oa3m $outfile</command> etc...
Galaxy throws Error: hhblits not found.
I've tried setting the PATH in the tool_dependencies/hhsuite/2.0.16/env.sh: #!/bin/bash # configure PATH to hhsuite binaries PATH="/opt/galaxy-dist/tool_dependencies/hhsuite/default/bin:$PATH" export PATH
still getting hhblits not found :-( What am I doing wrong?
Isabelle
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Hi Isabelle, Not sure about specifying the absolute path for the tool dependency dir, but I always use it. Also, my env.sh neither has a #!/bin/bash shebang line, nor quote marks around the tool path. If you are in the hhsuite/default/ dir and source env.sh, can you then run hhblits yourself (as galaxy user, or whoever owns the tools)? cheers, — Jorrit Boekel Proteomics systems developer BILS / Lehtiö lab Scilifelab Stockholm, Sweden On 31 May 2014, at 01:53, Isabelle Phan <isabelle.phan@seattlebiomed.org> wrote:
Hello,
I'm following "Managed Tool Dependencies" to the letter and still can't get Galaxy to find the executable. Is this page https://wiki.galaxyproject.org/Admin/Config/ToolDependencies up to date? If yes, what am I doing wrong?
Any help greatly appreciated!
# universe_wsgi.ini # I also tried the absolute path, it made no difference tool_dependency_dir = tool_dependencies
# tool_dependencies is set like instructed:
$ ls tool_dependencies/hhsuite/ 2.0.16/ default@ $ ls tool_dependencies/hhsuite/2.0.16/bin
ffindex_build* ffindex_get* hhalign* hhblits* hhconsensus* hhfilter* hhmake* hhsearch*
My tool: <tool id="hhpred_hhblits_01" name="Create MSA from single fasta for hhsearch" hidden="false" version="1.0.0" force_history_refresh="true"> <requirement type="package">hhsuite</requirement> <description>Searches single fasta iteratively against hmm db to build a MSA</description> <command>hhblits -i $input_file -d $database -oa3m $outfile</command> etc...
Galaxy throws Error: hhblits not found.
I've tried setting the PATH in the tool_dependencies/hhsuite/2.0.16/env.sh: #!/bin/bash # configure PATH to hhsuite binaries PATH="/opt/galaxy-dist/tool_dependencies/hhsuite/default/bin:$PATH" export PATH
still getting hhblits not found :-( What am I doing wrong?
Isabelle
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
participants (3)
-
Björn Grüning -
Isabelle Phan -
Jorrit Boekel