Re: [galaxy-dev] stdout in history
Hi Neil, I've only used this with my own tools, but basically it looks like: command whatever_your_tool_has_now /dev/null /command where /dev/null discards the output. Best, Wolfgang On 31.05.2014 01:11, neil.burd...@csiro.au wrote: Yes that would work. Can you supply an example if possible please? Thanks Neil Message: 3 Date: Fri, 30 May 2014 15:04:47 +0200 From: Wolfgang Maier wolfgang.ma...@biologie.uni-freiburg.de To: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] stdout in history Message-ID: lm9vle$70e$2...@ger.gmane.org Content-Type: text/plain; charset=UTF-8; format=flowed you could just redirect stdout to /dev/null in the tool's xml command line ? Is that an option for you ? Cheers, Wolfgang On 30.05.2014 14:35, neil.burd...@csiro.au wrote: Hi, It seems that the first 4/5 lines that are printed in the source code tools appear in the history (when expended) and in stdout link. Is there anyway to stop print statements appearing in the history panel? Thanks Neil ___ 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/
Re: [galaxy-dev] stdout in history
Hi Neil, I had some problems with this before too, so I created an tool config option a long time ago in my own galaxy fork. Never really bothered with submitting it, but it lives in these commits: https://bitbucket.org/glormph/adapt/commits/4ba256a9b8782642429ecb5472a456584bed86d5 https://bitbucket.org/glormph/adapt/commits/86ec8b1cfeb737dfa31a1b6faf18d918bea7b4c3 I started implementing it in datatypes (first commit), but moved it to tool config instead. If this is really interesting I guess I can submit a pull request, but it felt a bit hacky at the time. cheers, — Jorrit Boekel Proteomics systems developer BILS / Lehtiö lab Scilifelab Stockholm, Sweden On 30 May 2014, at 14:35, neil.burd...@csiro.au wrote: Hi, It seems that the first 4/5 lines that are printed in the source code tools appear in the history (when expended) and in stdout link. Is there anyway to stop print statements appearing in the history panel? Thanks Neil ___ 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/ ___ 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/
Re: [galaxy-dev] tool dependencies fail
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.p...@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=packagehhsuite/requirement descriptionSearches single fasta iteratively against hmm db to build a MSA/description commandhhblits -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/ ___ 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/
