[galaxy-dev] June 2014 Galaxy Update Newsletter: GCC2014 registration closes in 1 week!
Hello all, The June 2014 Galaxy Update Newsletter https://wiki.galaxyproject.org/GalaxyUpdates/2014_06 is out! There's a lot going on in the project and the community right now. The big news for the coming month is - *GCC2014 registration closes June 6! https://wiki.galaxyproject.org/GalaxyUpdates/2014_06#GCC2014:_June_30_-_July_2.2C_Baltimore* - (OK, that's a lie, but after June 6, late registration rates kick in, and you really don't want to pay those.) - *GCC2014 starts June 30 https://wiki.galaxyproject.org/GalaxyUpdates/2014_06#GCC2014:_June_30_-_July_2.2C_Baltimore!* - *The first ever GCC Hackathon starts June 28 https://wiki.galaxyproject.org/GalaxyUpdates/2014_06#Galaxy_Hackathon_at_GCC2014!* - After a very long and productive life, the *Galaxy-User mailing list is retiring on June 6* https://wiki.galaxyproject.org/GalaxyUpdates/2014_06#Galaxy-User_Being_Retired_June_6. (Don't worry. It's been replaced by Galaxy Biostar https://wiki.galaxyproject.org/GalaxyUpdates/2014_06#Galaxy-User_Being_Retired_June_6 .) There are also at least 14 other Galaxy related events https://wiki.galaxyproject.org/GalaxyUpdates/2014_06#Other_Events in the next two months in Thailand, Canada, France, the United States, Italy, the Netherlands, Australia, and Brazil. And, in the past month there were: - 49 new papers https://wiki.galaxyproject.org/GalaxyUpdates/2014_06#New_Papers - One new public server (deepTools) https://wiki.galaxyproject.org/GalaxyUpdates/2014_06#New_Public_Servers - One new Galaxy deployment description (deepTools) https://wiki.galaxyproject.org/GalaxyUpdates/2014_06#Galaxy_Community_Hubs - and a stunning number of ToolShed contributions https://wiki.galaxyproject.org/GalaxyUpdates/2014_06#ToolShed_Contributions Please let us know if you have anything to include in the July newsletter, and we will see you in Baltimore! Dave Clements and the Galaxy Team https://wiki.galaxyproject.org/GalaxyTeam -- http://galaxyproject.org/GCC2014 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/ ___ 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/
[galaxy-dev] stdout in history
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
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/
[galaxy-dev] stdout in history
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 -- ___ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ End of galaxy-dev Digest, Vol 95, Issue 29 ** ___ 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/
[galaxy-dev] tool dependencies fail
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/
Re: [galaxy-dev] tool dependencies fail
Hi, can you try: requirements requirement type=packagehhsuite/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=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/
