- galaxy-dev - lists.galaxyproject.org

Python 2.7 vs 2.6 for galaxy after 16.01
by D K 24 Mar '16

24 Mar '16

Hi Galaxy Devs, This may be premature but I read that for Galaxy after 16.01 that the plan is for python 2.6 to no longer be supported. I'm currently running CentOS 6.6 which uses python 2.6. In order to be able to use newer versions of Galaxy is my only option to upgrade to a newer version of CentOS? Is it possible to use Conda, RedHat Software Collections or some other similar method instead of doing this upgrade? Thanks!

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Data set too large
by Tiara Smith 23 Mar '16

23 Mar '16

Hell I am accessing galaxy from a main computer on my university campus. I am having difficulty uploading my exome files and keep getting the following error prompt: ndex30_CACCGG_L001-L002_R1_001.bam *2.8* GB Auto-detect ----- Additional Species Are Below ----- *Failed: *File exceeds 2GB. Please use a FTP client. Is there a way to increase my file upload limit? my data sets range from 1.9GB ro 3.9GB. thank you for your help. Tiara Smith

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automatic adding of a tab in a fastq header
by Fabien Mareuil 23 Mar '16

23 Mar '16

Hi, We got a problem with the new version of Data libraries. When we upload a fastq file from a User Directory, a tabulation character is added in the header in replacement of a space character. from @HWI-D00395:188:HYGNFADXX:2:1108:1315:1965 1:N:0:ATGAGC to @HWI-D00395:188:HYGNFADXX:2:1108:1315:1965 1:N:0:ATGAGC This behavior causes an error with cutadapt 1.6 (maybe with other tools) because it doesn't work with tab character. With the direct upload tool or the deprecated version of Data Libraries no tab character is added.Do you have some idea to correct this problem? Thanks a lot Best regards -- Fabien Mareuil | Centre d'Informatique pour la Biologie fabien.mareuil(a)pasteur.fr <mailto:fabien.mareuil@pasteur.fr> | Institut Pasteur 25,28 rue du Docteur Roux 75015 Paris, France

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perl version 5.18.1 repository error
by Rathert, Philipp, Dr. 23 Mar '16

23 Mar '16

Dear all, i am trying to install tool (meme-fimo) which needs package_perl_xml_parser_expat_2_41 that has a pearl 5.18.1 dependency. however, although the tool installs just fine it shows that package_perl_xml_parser_expat_2_41 has missing dependencies: Tool shed repository:package_perl_xml_parser_expat_2_41 Tool shed repository changeset revision:1ce3818a8eb9 Tool dependency status:Error Tool dependency installation error:Error installing tool dependency perl version 5.18.1: Unable to locate the repository directory for revision d905bb415eca of installed repository package_perl_5_18 owned by iuc. Tool dependency installation directory:././tool_deps/perl/5.18.1/iuc/package_perl_xml_parser_expat_2_41/1ce3818a8eb9 Is this an error of my local instance or is the revision missing on the toolshed? Thank you very much for your help. Cheers, philipp

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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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