- galaxy-dev - lists.galaxyproject.org

Tool Shed packages for BLAST+ binaries
by Peter Cock 03 Sep '13

03 Sep '13

Hi Greg et al, For the NCBI BLAST+ wrappers, Nicola has suggested we split out the binaries themselves into a separate Tool Shed package, e.g. package_blast_plus_2_2_26 and similar for the later releases. https://github.com/peterjc/galaxy_blast/issues/7 I think this is a good idea. I'd like to check if there are any complications foreseeable from the fact that the NCBI BLAST+ wrappers were migrated out of the Galaxy core and therefore have migration scripts we need to consider. Potentially this could be held under the shared IUC account as planned for other commonly used packages? Or would the migration issues require it to also live under devteam? Also, we may wish to add a dependency on BOOST, e.g. http://testtoolshed.g2.bx.psu.edu/view/iuc/package_boost_1_53 once this is on the main Tool Shed. Regards, Peter

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[GSoC2013] Week 9,10,11 Update
by Saket Choudhary 02 Sep '13

02 Sep '13

Update here : http://galaxy-gsoc2013.blogspot.in/2013/09/blog-post.html -- Saket

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Postgresql database cleaning
by Christophe Antoniewski 01 Sep '13

01 Sep '13

Hi everybody, The python scripts to clean histories, datasets, users etc.. are fine... However, the records are not really removed from the postgresql database and as a result, this one gets bigger and bigger with unused records. Ours is above 1 To after 2 years of production. Is there a safe way to clean the database from unused records and their dependencies to reduce it size, without being a postgresql guru ? Chris -- Christophe Antoniewski Drosophila Genetics and Epigenetics Laboratoire de Biolologie du Développement 9, Quai St Bernard, Boîte courrier 24 75252 Paris Cedex 05 Tel +33 1 44 27 34 39 Fax +33 1 44 27 34 45 Mobile +33 6 68 60 51 50 http://drosophile.org

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Re: [galaxy-dev] [galaxy-user] About tool classify in the tool box panel
by Björn Grüning 01 Sep '13

01 Sep '13

Hi, try that: <label text="GFF" id="gff" /> Cheers, Bjoern > Dear Bjoern > > > I know that the "name" define sections name, however what I want to > fulfill is to part section into several groups. Just like the > following figure shows. > > > 内嵌图片 1 > > > I want to add the "NGS TOOLBOX BETA" and "REGENETICS"--- this kind of > classify function. > > > Do you know how to fulfill it in my local Galaxy? > > > Thank you for your reply. > > > Regards, > XiaoTao > > > > 2013/8/31 Bjoern Gruening <bjoern.gruening(a)gmail.com> > Hi Xiao, > > have a look in your tool_conf.xml file. > > <section name="Send Data" id="send"> > <tool file="data_destination/epigraph.xml" /> > <tool file="data_destination/epigraph_test.xml" /> > <tool file="genomespace/genomespace_exporter.xml" /> > </section> > > You can specify sections with the section tag. Keep in mind > that the ID > needs to be unique. > > Cheers, > Bjoern > > > Dear all > > > > > > I want to know how to part the tool panel into several group > just like > > the public Galaxy. It classify the tools into NGS Tools Box > and > > RECENTS. I can not find tag that up <section> tag in the > wiki > > document. Anyone can tell me how to configure to classify > tools? > > > > > > Thank you for all your help > > > > > > Regards, > > Xiaotao JIANG > > The University of HongKong > > > ___________________________________________________________ > > The Galaxy User list should be used for the discussion of > > Galaxy analysis and other features on the public server > > at usegalaxy.org. Please keep all replies on the list by > > using "reply all" in your mail client. For discussion of > > local Galaxy instances and the Galaxy source code, please > > use the Galaxy Development list: > > > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > > > 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/ > > > > >

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URL problem
by Jennifer Jackson 30 Aug '13

30 Aug '13

Hi Alper, There may be permissions problems if just for these two links, but I am not an expert on this. Moving post over to the galaxy-dev list, which will give it better exposure to the development team and community. You'll want to post here directly with any future local install questions. http://wiki.galaxyproject.org/Support#Mailing_Lists Best, Jen Galaxy team On 8/26/13 10:49 AM, Kucukural, Alper wrote: > Hi, > I have a problem in galaxy to get host/domain name in two different pages. > First one is in the tool installation from toolshed, I got the error below, > > ##### > Not Found > > The requested URL /admin_toolshed/prepare_for_install was not found on this server. > > ##### > > The second one is in the saved histories. When I click the buttons of the saved histories. I got the similar error like below. > ##### > Not Found > > The requested URL /history/list was not found on this server. > > ##### > > I haven't seen these any other pages yet. > > My installation is working on LDAP authentication with Proxy. So, I could not find a place to set the domain or host name in these two places that they can actually find the requested URLs. > > In the paster.log file. I don't get any error when I install a tool or go to another history. It doesn't report any error. > > Thanks for your help, > > Alper Kucukural > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > 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/ -- Jennifer Hillman-Jackson http://galaxyproject.org

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August 2013 Galaxy Update Newsletter is out
by Dave Clements 30 Aug '13

30 Aug '13

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Re: [galaxy-dev] Local installation: Uploading fastq file takes ages - why?
by Nate Coraor 30 Aug '13

30 Aug '13

On Aug 14, 2013, at 8:39 AM, Boaz Shaanan wrote: > Hi, > > On my local galaxy installation (updated to the latest version yesterday), it takes ages (hours!) to upload a fastq files. I attach a report from the the computer on which galaxy is installed. The fastq file is uploaded from > 132.72.88.186. Initially there is an error message (the attached file also includes the debug url at the end) and after a while the upload proceeds but takes very long time. Transferring the file by sftp between the two computers takes only seconds. > Is there anytning wrong with my installation (i.e. something is not properly defined or something like this). Hi Boaz, Could you make sure that debug and use_interactive are both set to False in universe_wsgi.ini? Thanks, --nate > > I'd appreciate your help. > > Boaz > > Boaz Shaanan, Ph.D. > Dept. of Life Sciences > Ben-Gurion University of the Negev > Beer-Sheva 84105 > Israel > > E-mail: bshaanan(a)bgu.ac.il > Phone: 972-8-647-2220 Skype: boaz.shaanan > Fax: 972-8-647-2992 or 972-8-646-1710 > > > > > <galaxy_local_server_error.txt>___________________________________________________________ > 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/

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adding new genome to local galaxy instance
by Vipin TS 30 Aug '13

30 Aug '13

Hello, I am slightly confused with adding a new genome to my local Galaxy instance, I am using the recent default branch 10411:c42567f43aa7 (following the documentation at http://wiki.galaxyproject.org/Admin/Data%20Integration) I have edited the ~/galaxy-dist/tool-data/all_fasta.loc to add new Arabidopsis genome and updated ~/galaxy-dist/tool-data/shared/ucsc/builds.txt, when I restarted my local instance, I am not finding the newly added genome in database. any idea what is going wrong here ? thanks, --/Vipin

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How to get the import of BAM files to create its index on the cluster
by Anthonius deBoer 30 Aug '13

30 Aug '13

Hi, I am looking how to improve the import of BAM files into galaxy. I often use the Upload tool in the Data Libraries to upload a number of BAM files into galaxy (after recombining several readgroups into a BAM file for the library, which I unfortunately have to do OUTSIDE of galaxy since it cannot take an arbitrary set of BAM files in a workflow)... The UPLOAD tool seems to be correctly submitted to the cluster as you would expect, but then it seems that SAMTOOLS is run on each of the BAM files to create a index file (even though the directory already has one) on the server that is running galaxy, i.e. locally! Is there a way to move the SAMTOOLS index creation into the upload tool so that it can be run in parallel on the cluster? Thanks Thon

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Better packaging for toolshed binaries
by Guest, Simon 29 Aug '13

29 Aug '13

Dear Galaxians, This email is about difficulties with the current approach for installing tool dependency binaries from the Galaxy Toolshed, and what might be done to improve the situation. It comes down to this: packaging software to run on different systems is tricky. It is a problem that has been solved by various Linux distributions with their packaging systems (RPM, deb, etc.), and package archives. The Galaxy Toolshed is trying to solve this problem again, but so far it doesn't work very well. There must be something better we can do. Since gaining a better understanding from the Galaxy Community Conference of what the Toolshed is trying to do (versioned tools, reproducibility), I have been working on switching over from locally installed tools to Toolshed versions. However, it has not gone well, and I think I am about to revert to my previous approach. Here's the problem: building software from source on any system requires certain tweaks to the build process which are dependent on the target platform. An example is the NCBI BLAST+ suite, which failed to build on my (EL6) system, because it couldn't run /usr/bin/touch. That's pretty dumb, and pretty simple to solve in isolation - it needs to be running /bin/touch instead. But the general point is this: it's not feasible (i.e. too much work, too hard) to produce build scripts to build software from source that work on any platform, even the common ones. Packaging source code for a given platform is a non-trivial task. The RPM and deb packagers are doing a good job here. It's a significant amount of work. I know that, as I've been packaging bioinformatics software as binary RPMs for EL6 for 18 months or so now, and have done nearly 300 packages. What do we want? Simply to be able to install a given version of some software, and all its dependencies, with a single click, or a single command, and have it Just Work (tm). It's the dependencies that make this hard. Things get installed in different ways on different systems. Does your platform need #include <bam.h>, or #include <bam/bam.h>? If the former, then you'll have to patch tophat, say, (in a trivial way) before building it. I think this is simply too hard to do by embedding some commands and conditionals in Toolshed XML build files. It seems to me that a number of people out there are currently having some issues installing tool dependencies from the Toolshed, because things are not building as expected. I think it's much easier for just one person to troubleshoot why things go wrong when they are packaging the software for a given platform, rather than for each end user (Galaxy admin) to wonder why a tool failed to install. So, what to do? My starting point is that I have packaged a large amount of bioinformatics software for EL6, which is freely available at http://rpm.agresearch.co.nz/. I'm after some Galaxy tool wrappers for the tools that we use here at AgResearch, which can simply make use of packages installed from this repo. Is there any interest in exploring the merits or otherwise of this approach in the Galaxy community? cheers, Simon Simon Guest Senior UNIX Technical Consultant AgResearch, New Zealand ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. =======================================================================

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