galaxy-dev March 2016

galaxy-dev@lists.galaxyproject.org

74 participants
98 discussions

Numpy 1.9 installation errors
by Dewell, Scott 22 Mar '16

22 Mar '16

Hi all - trying to install numpy 1.9 and getting the following error: numpy 1.9 package Error Error installing tool dependency numpy version 1.9: 'NoneType' object has no attribute 'prepare_step' atlas 3.10.2 package Installed numpy 1.9 package Error Error installing tool dependency numpy version 1.9: 'NoneType' object has no attribute 'prepare_step' python 2.7.10 package Installed numpy 1.7 has installed successfully elsewhere. Thank you!

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GCC2016 Oral Presentation Abstracts due this Friday, March 25
by Dave Clements 22 Mar '16

22 Mar '16

Hello all, The general announcement for GCC2016 is below. Please note: 1) The oral presentation abstract deadline <https://gcc2016.iu.edu/abstracts/index.php> is March 25, *this Friday.* 2) There are scholarships available <https://wiki.galaxyproject.org/News/GCC2016Scholarships> for students and post-docs in historically underrepresented groups. And, please distribute the announcement below to any groups or individuals who might be interested, Thanks, and hope to see you in Bloomington, Dave C --------------------- The *2016 Galaxy Community Conference *(*GCC2016*, *gcc2016.iu.edu <http://gcc2016.iu.edu/>*) features two days of presentations, discussions, poster sessions, lightning talks, computer demos, keynotes, and birds-of-a-feather meetups, *all about data-intensive biology and the tools that support it*. Keynote speaker Yoav Gilad <http://genes.uchicago.edu/directory/yoav-gilad-phd/>, a professor of human genetics at the University of Chicago, will kick-start the main conference with a discussion on the analysis of large gene regulatory data sets. Preconference events include data <https://gcc2016.iu.edu/hacks/hacks-data.php> and coding <https://gcc2016.iu.edu/hacks/hacks-coding.php> hackathons <https://gcc2016.iu.edu/hacks/index.php>, and *two days of training* <https://gcc16.sched.org/overview/type/Training+%E2%80%94+Any> in five concurrent tracks covering 26 topics. *GCC2016* will be held at *Indiana University* in Bloomington, Indiana, June 25-29, 2016. Since it started seven years ago, GCC has been a well-attended gathering of biologists, genome researchers, bioinformaticians, and others in data-intensive biomedical research around the world. Galaxy <https://galaxyproject.org/> is an open, web-based platform for data-intensive biomedical research and enables easy interactive analysis through the web on arbitrarily large data sets. The Galaxy framework is a major resource in achieving key research goals within the biological field. It provides next-generation sequencing (NGS) tools and workflows for short-read mapping, ChIP-seq, RNA-seq, metagenomics, variant analysis, visualization, and support for Galaxy in the cloud. There are hundreds of local installs, and *over 80 publicly accessible servers* around the world. *Abstract submission** for oral presentations closes March 25. *Abstract submission for posters and computer demonstrations closes May 20. *Early registration* is now open. Registration starts at less than $45/day for post-docs and students. Registering early assures you a place at the conference and also a spot in the training workshops <https://gcc16.sched.org/overview/type/Training+%E2%80%94+Any> you want to attend. You can also *book conference housing* when you register. *Registration and lodging scholarships <https://wiki.galaxyproject.org/News/GCC2016Scholarships>* are available for attendees from underrepresented groups and developing countries. Thanks, and we hope to see you in Bloomington! The *GCC2016 Exec* -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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"Edit settings" button in Trackster is no longer working (15.10)
by Hans-Rudolf Hotz 22 Mar '16

22 Mar '16

Hi all Since we upgraded our Galaxy installation from 15.05 to 15.10 (plus the recent security fix, changeset: 17161:3f95c21b1a85), the "Edit settings" button in Trackster is no longer working. The window, which normally allows you to select the colors, etc. doesn't show up anymore. This happens with different browsers on mac and linux. On the console I get: "TypeError: a.browser is undefined" Has anyone else seen this problem? Or is there even already a fix available? Thank you very much for your help Hans-Rudolf -- Hans-Rudolf Hotz, PhD Bioinformatics Support Friedrich Miescher Institute for Biomedical Research Maulbeerstrasse 66 4058 Basel/Switzerland

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shed_tool_conf.xml
by Rathert, Philipp, Dr. 22 Mar '16

22 Mar '16

Dear all, I think I made a really stupid mistake. I edited the shed_tool_con.xml file to change the order and section of tools. Doing this I might have introduced an error I cannot locate. However (now comes the stupidity), I didn't save the old version of the shed_tool_conf.xml file... Is there a way to fix this or do I have to reinstall all tools again? Thank you for your help. cheers, Philipp

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Re: [galaxy-dev] shed_tool_conf.xml
by Rathert, Philipp, Dr. 22 Mar '16

22 Mar '16

Hi Peter, thx for the hint. Xcode was very helpful and I could localize the error. However, this couldn't tell me why my label ids didn't work. how do I implement those. Does this need a delimiter at the end like the sections? <label id="basic_tools" text="Basic Tools" version="" /> Cheers, Philipp -----Original message----- From: Peter Cock <p.j.a.cock(a)googlemail.com> Sent: Tuesday 22nd March 2016 12:56 To: Rathert, Philipp, Dr. <philipp.rathert(a)ibc.uni-stuttgart.de> Cc: galaxy-dev(a)lists.galaxyproject.org Subject: Re: [galaxy-dev] shed_tool_conf.xml I would try validating the broken XML file (e.g. using an online tool, or an XML aware editor). That might be enough to find the error and fix it by hand. I don't know if there is a clever way to regenerate the file instead... Peter On Tue, Mar 22, 2016 at 11:49 AM, Rathert, Philipp, Dr. <philipp.rathert(a)ibc.uni-stuttgart.de> wrote: > Dear all, > > > I think I made a really stupid mistake. I edited the shed_tool_con.xml file > to change the order and section of tools. > > > Doing this I might have introduced an error I cannot locate. However (now > comes the stupidity), I didn't save the old version of the > shed_tool_conf.xml file... > > > Is there a way to fix this or do I have to reinstall all tools again? > > > Thank you for your help. > > > cheers, > > > Philipp > > > ___________________________________________________________ > 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: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/

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Re: [galaxy-dev] mirDeep2 install error
by Jochen Bick 22 Mar '16

22 Mar '16

Now it worked! I had to purge the old squid version 1.9g version because it still recognised the old one to be not correctly installed... Thanks Jochen On 22.03.2016 11:26, Bjoern Gruening wrote: > Can you remove and reinstall > > package_randfold_2_0 > > Hopefully this solves your problem, > Cheers, > Bjoern > > > On 22.03.2016 11:21, Jochen Bick wrote: >> Hej Björn, >> >> so it did work in the development galaxy but not in our production >> galaxy. Here I get the following error in package_randfold_2_0 after >> successfully installing squid version 1.9g : >> >> randfold.c:24:18: error: squid.h: No such file or directory >> randfold.c:26:23: error: sre_random.h: No such file or directory >> randfold.c: In function 'main': >> randfold.c:30: error: 'SQFILE' undeclared (first use in this function) >> randfold.c:30: error: (Each undeclared identifier is reported only once >> randfold.c:30: error: for each function it appears in.) >> randfold.c:30: error: 'sqfp' undeclared (first use in this function) >> randfold.c:38: error: 'SQINFO' undeclared (first use in this function) >> randfold.c:38: error: expected ';' before 'sqinfo' >> randfold.c:89: warning: incompatible implicit declaration of built-in >> function 'strcpy' >> randfold.c:96: error: 'SQFILE_FASTA' undeclared (first use in this >> function) >> randfold.c:100: error: 'sqinfo' undeclared (first use in this function) >> randfold.c:103: warning: incompatible implicit declaration of built-in >> function 'malloc' >> randfold.c:103: warning: incompatible implicit declaration of built-in >> function 'strlen' >> randfold.c:136: warning: incompatible implicit declaration of built-in >> function 'fabs' >> randfold.c:158: warning: incompatible implicit declaration of built-in >> function 'free' >> make: *** [randfold] Error 1 >> >> Cheer Jochen >> >> >> ___________________________________________________________ >> 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: >> https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ >

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mirDeep2 install error
by Jochen Bick 22 Mar '16

22 Mar '16

Hi, I tried to install suite_mirdeep_2_0. There is an error in the dependencies of package_squid_1_9g the download link has change to http://eddylab.org/software/squid/squid.tar.gz Cheers Jochen

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Error filtering sam files
by Juan Vladimir de la Rosa Medina 21 Mar '16

21 Mar '16

Hi guys, when I try to run "Filter SAM or BAM, output SAM or BAM" from SAMtools on our local galaxy instance, we get this error: Traceback (most recent call last): File "/home/jvdelarosa/Bioinformatica/Software/galaxy/lib/galaxy/jobs/runners/__init__.py", line 166, in prepare_job job_wrapper.prepare() File "/home/jvdelarosa/Bioinformatica/Software/galaxy/lib/galaxy/jobs/__init__.py", line 889, in prepare self.command_line, self.extra_filenames, self.environment_variables = tool_evaluator.build() File "/home/jvdelarosa/Bioinformatica/Software/galaxy/lib/galaxy/tools/evaluation.py", line 442, in build raise e ValueError: invalid literal for int() with base 16: '' Enviado desde Correo para Windows 10

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per-tool job resource defaults
by Stephan Oepen 21 Mar '16

21 Mar '16

dear colleagues, at the university of oslo, we develop a galaxy-based portal for natural language processing (LAP: Language Analysis Portal). jobs are submitted to a compute cluster via DRMAA and SLURM. current development is against the galaxy release of march 2015. i am wondering about fine-grained control of job resources. our goal is that most users need not look past the ‘Use default job resource parameters’ toggle in the job configuration dialogue. as i understand it, i think we can populate the ‘nativeSpecification’ parameter in ‘job_conf.xml’ with SLURM-specific command-line options to set defaults, for example the project, maximum run-time, number of cores, memory per core, and such. i assume these defaults will be combined with and overwritten by ‘custom’ job resource parameters, in case any are specified in the job configuration dialogue? i tried to track the flow of information from ‘lib/galaxy/jobs/runners/drmaa.py’ via ‘scripts/drmaa_external_runner.py’ into the drmaa-python egg, but i could not easily work out where the merging of ‘nativeSpecification’ and custom resource parameters happens; presumably at about the same time as an actual job script file is created, for submission to SLURM? could someone point me in the right direction here? —more importantly, maybe: we would like to establish per-tool resource defaults. for example, some of our tools require substantially more memory per core than others. i cannot easily find a way of associating resource default with individual tools. i looked at the tool configuration syntax, ‘job_conf.xml.sample_advanced’, and ‘job_resource_params_conf.xml.sample’, as well as at the following documentation pages: https://wiki.galaxyproject.org/Admin/Config/Jobs https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster i am hoping i am overlooking something :-). is there a way to define job resource defaults on a per-tool basis? with warmest thanks in advance, oe

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Problem with tool dependency
by Mikael Loaec 21 Mar '16

21 Mar '16

Hi, We, actually have problems with installation of some tools using the galaxy web interface or the API throught the script install_tool_shed_tools.py ( https://github.com/galaxyproject/ansible-galaxy-tools/blob/master/files/ins… ). When a tool has a package dependency, the dependency is installed, but the env.sh of this dependency is not sourced at the end of its installation and before the installation of the parent tool. So the dependency is installed, but the parent tool installation failed because it needs the env.sh of the depency sourced. For example for GATK : When we install GATK, it looks up for R, which is installed correctly but its path is not sourced so GATK installation failled. Any idea ? Do we have a problem in our configuration or it's a known problem ? Thanks in Advance for your response. Regards, Mikael & Françoise URGI INRA

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galaxy-dev March 2016