August 2013 - galaxy-dev - lists.galaxyproject.org

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 29 Aug '13

29 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 29 Aug '13

29 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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No zebrafish Zv9 build
by Smith, Tiffany L 29 Aug '13

29 Aug '13

I cannot work with Zv9 data because galaxy does not seem to support it. Can you please add Zv9/danRer7 to the database/build list? Tiffany Smith

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Re: [galaxy-dev] adding new genome to local galaxy instance
by Ricardo Perez 29 Aug '13

29 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 Dear Vipin, Have you restarted your galaxy server? You need to restart so galaxy's can be updated. --Ricardo Perez

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Local Instance and current website are not the same
by Tevfik Hamdi Kitapci 29 Aug '13

29 Aug '13

Hi, I installed a local instance of galaxy browser on my local machine using the steps in: http://wiki.galaxyproject.org/Admin/Get%20Galaxy I tried both the default (hg update default) and stable versions (hg update stable) but the current website has different features on the left panel then the local instance that I downloaded. Specifically I want to use the SnpEff feature under the NGS toolbox Beta on the left panel of the website. But I can't find this feature on the local instance is there anyway to install a local instance of the current version of the website? Thanks Best Regards Hamdi Kitapci

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Patch for RPy for R 3.0.1
by Guest, Simon 29 Aug '13

29 Aug '13

Just catching up with the galaxy-dev mailing list, and found some remarks about RPy not working with R 3.0. If that's bugging you, you may be interested in my patches for RPy-1.0.3a, which enable it to work with R 3.0.1 (and probably 3.0.0, but we've moved on from that here). Attached, in case it helps someone. cheers, Simon PS: Anyone on EL6 could just install the python-rpy package from the AgResearch repo, http://rpm.agresearch.co.nz/ ;-) ======================================================================= 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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tool not runing in workflow
by Berner, Thomas 27 Aug '13

27 Aug '13

Hey guys, we installed and used a tool of the mothur_toolsuite in our local galaxy instance named "get.otulist", but if we want to integrate it into a workflow (extract from history) we get the following error for the next step: "Error due to input mapping of 'Join two datasets' in '__new_primary_file_logfile|0.03.otu__'. A common cause of this is conditional outputs that cannot be determined until runtime, please review your workflow." In the workflow editor only the *.html file is displayed as output but not the tabular file which is generated by the tool normally. There should be an output (tabular) which we want to join with another one, but this doesn't work in the workflow. Can somebody give me a hint for this? Greetings, Thomas

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