[galaxy-dev] googlebot
Hi, my paster.log is full of errors relating to a googlebot trying to access a library file. I noticed a robots.txt file in the static folder configured as such. User-agent: * Disallow: / I thought this would stop all bots accessing all files. Should this be configured differently? Thanks Shaun -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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/
Re: [galaxy-dev] Divide FASTQ file into paired and unpaired reads (version 0.0.4) - naming suffix not recognized
Hi Peter, Thanks! The fix worked with the new Illumina format. Your help is much appreciated :) Cheers, Liisa Liisa Koski Bioinformatics Programmer From: Peter Cock p.j.a.c...@googlemail.com To: Liisa Koski liisa.ko...@dnalandmarks.ca Cc: galaxy-dev galaxy-...@bx.psu.edu Date: 2011-12-12 03:47 Subject: Re: [galaxy-dev] Divide FASTQ file into paired and unpaired reads (version 0.0.4) - naming suffix not recognized On Friday, December 9, 2011, Peter Cock p.j.a.c...@googlemail.com wrote: On Fri, Dec 9, 2011 at 5:05 PM, Liisa Koski liisa.ko...@dnalandmarks.ca wrote: Thanks Peter! That would be great! Let me know when you want me to test it :) Cheers, Liisa The revised code is here on bitbucket (on the branch tools), you'll need fastq_paired_unpaired.py and fastq_paired_unpaired.xml v0.0.5: Try this (looks like I had the wrong link on Friday), sorry: https://bitbucket.org/peterjc/galaxy-central/src/a25f7920a1e5/tools/fastq Peter ___ 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/
Re: [galaxy-dev] Galaxy on GPU
On Dec 9, 2011, at 5:58 PM, Isabelle Phan wrote: Hello, Can any applications in Galaxy use GPU hardware (e.g. for processing next gen data)? Hi Isabelle, None of the tools bundled in Galaxy currently make use of a GPU because afaik, none of them support it (although there have been some attempts, see: http://seqanswers.com/forums/showthread.php?t=13497 ). If any tool that can run on a GPU is added to Galaxy, it could be scheduled to run on that specific hardware via Galaxy's existing job running mechanisms, however. --nate Thanks, Isabelle PS: From Enis's reply to a post from last year, it looked like the answer was no at the time On Fri, Dec 10, 2010 at 8:59 PM, [hidden email] wrote: Original Message Subject: Re: [galaxy-dev] Wiki erratum... From:Richard Bruskiewich [hidden email] Date:Fri, December 10, 2010 7:17 pm To: Anton Nekrutenko [hidden email] -- Also, Amazon has so-called cluster instances, and now GPU cluster instances. Again, the same idea applies: can specific tools be told to only run on such a cluster instance? Further ahead, could Galaxy be configured to automatically start/stop specific instances only when needed (including cluster instances)? Because MPI-type jobs are the only true beneficiaries of the cluster instances, but only a handful of bioinformatics software are actually implemented using MPI and because those instances require a different AMI, we do not currently have support for that type of instances - maybe down the line. Nonetheless, in the coming new version Galaxy Cloud (currently being tested), the application will be able to automatically scale the size of the cluster based on the current workload. -- Isabelle Phan, DPhil Seattle Biomedical Research Institute +1(206)256 7113 ___ 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/ ___ 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/
Re: [galaxy-dev] How and where to install tool dependencies
On Dec 9, 2011, at 4:34 PM, Josh Nielsen wrote: Hello, I have a question which I have not seen specifically addressed in the online Galaxy wiki documentation about how to integrate tools (dependencies) into Galaxy. I have implemented a locally managed instance of Galaxy that my business is using with our cluster and now have a freshly installed and configured instance of Galaxy running. It is bare-bones right now and I did not use mercurial to sync any existing files/directory structures. I have seen the page on external tool dependencies (http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies) needed for Galaxy, but I am somewhat unsure where to place the tools to utilize them as intended (other than through trial error). It appears that there are shell directories for the tools under ~/galaxy-dist/tools/ with basic wrapper scripts but without the corresponding executables (very few that I've noticed have the tools already in them). Is the intent to download the dependency tools and (building from source if necessary) take the binaries in those directories and copy them to their corresponding directory under ~/galaxy-dist/tools/? This seems to have worked with an error I first got when clipping a FASTQ file which reported that fastx_clipper was not a recognized command. So I downloaded the FASTX Toolkit, compiled the binaries, and copied only the binaries into the corresponding fastx tools directory. Would I do the same thing for TopHat and Cufflinks by taking all their binaries (combined) and copying them into ~/galaxy-dist/tools/ngs_rna/? Hi Josh, There are two ways to do this. The simplest is to place the binaries into a directory on the Galaxy user's $PATH. The second is via the tool dependency system, which I need to write up documentation for to put in the wiki, which I'll do this week. Even if that is the case though, I have occasionally gotten errors about tools missing in completely different directories. One was for the FASTQ Groomer. One user saw this error in their browser (which for now is the only way I know to figure out where tools are *expected* to be): File /home/galaxy/galaxy-dist/tools/rgenetics/rgFastQC.py, line 141, in assert os.path.isfile(opts.executable),'##rgFastQC.py error - cannot find executable %s' % opts.executable AssertionError: ##rgFastQC.py error - cannot find executable /home/galaxy/galaxy-dist/tool-data/shared/jars/FastQC/fastqc Java JARs are a special case, and FastQC has a unique way of locating its jars, which is why it is expected to be found in that directory. This needs to be documented. To fix this I downloaded the FastQC tar file from its webpage, unzipped it, and copied the fastqc binary/script to the home/galaxy/galaxy-dist/tool-data/shared/jars/FastQC/ directory. I also had to mkdir FastQC/ under jars/ to place it there since it didn't already exist. Had I not been told the specific directory by the error I'm not sure how I would have intuitively known to place the binary there (unless I'm overlooking some critical documentation). And how do I know that other similar things are not missing which should be there? Can anyone shed some light on this please? Adding a brief page on the Galaxy wiki site under the Admin section about this would really help, even if it only showed an example for one or two specific tools. The list of external dependencies by tool is maintained here: http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies I'll update this page with links to the new documentation when I write it. I should also add that work is under way to make it possible to automatically install these dependencies as needed. --nate Thanks, Josh ___ 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/ ___ 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/
Re: [galaxy-dev] Tools accessing web services
Hi Amelia, Sorry for the delay in reply. Could you provide a copy of your xml file and we can take a look. Thanks for using Galaxy, Dan On Nov 21, 2011, at 12:26 PM, Amelia Ireland wrote: Can anyone answer this, please, or point me to the relevant documentation? On 07/11/2011, Amelia Ireland airel...@lbl.gov wrote: Apologies in advance for the newbie question. I have a script that uses various UniProt web services. The script sends off a request to the UniProt server, waits for it to be returned, and then writes the results to a file. This works fine as a standalone script, but when plugged into Galaxy, I get this error: ⇝ KeyError: 'GALAXY_URL' URL: http://127.0.0.1:8080/tool_runner/index Does Galaxy intervene in the operation of all tools that access outside web services, and if so, do I need to rewrite the tool as one that acts as a data source (like the UCSC browser, biomart, etc.)? The data sources documentation did not mention whether this was necessary or not. Thanks! -- Amelia Ireland Scientific Curator, Gene Ontology project http://www.berkeleybop.org || http://www.geneontology.org Preventing Euthanasia Through Rescue: http://petrescueinc.org -- Amelia Ireland Scientific Curator, Gene Ontology project http://www.berkeleybop.org || http://www.geneontology.org Preventing Euthanasia Through Rescue: http://petrescueinc.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/ ___ 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/
Re: [galaxy-dev] How and where to install tool dependencies
Thanks Nate! Updated documentation is always welcome and useful. I appreciate the clarifications. -J On Mon, Dec 12, 2011 at 10:18 AM, Nate Coraor n...@bx.psu.edu wrote: On Dec 9, 2011, at 4:34 PM, Josh Nielsen wrote: Hello, I have a question which I have not seen specifically addressed in the online Galaxy wiki documentation about how to integrate tools (dependencies) into Galaxy. I have implemented a locally managed instance of Galaxy that my business is using with our cluster and now have a freshly installed and configured instance of Galaxy running. It is bare-bones right now and I did not use mercurial to sync any existing files/directory structures. I have seen the page on external tool dependencies ( http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies) needed for Galaxy, but I am somewhat unsure where to place the tools to utilize them as intended (other than through trial error). It appears that there are shell directories for the tools under ~/galaxy-dist/tools/ with basic wrapper scripts but without the corresponding executables (very few that I've noticed have the tools already in them). Is the intent to download the dependency tools and (building from source if necessary) take the binaries in those directories and copy them to their corresponding directory under ~/galaxy-dist/tools/? This seems to have worked with an error I first got when clipping a FASTQ file which reported that fastx_clipper was not a recognized command. So I downloaded the FASTX Toolkit, compiled the binaries, and copied only the binaries into the corresponding fastx tools directory. Would I do the same thing for TopHat and Cufflinks by taking all their binaries (combined) and copying them into ~/galaxy-dist/tools/ngs_rna/? Hi Josh, There are two ways to do this. The simplest is to place the binaries into a directory on the Galaxy user's $PATH. The second is via the tool dependency system, which I need to write up documentation for to put in the wiki, which I'll do this week. Even if that is the case though, I have occasionally gotten errors about tools missing in completely different directories. One was for the FASTQ Groomer. One user saw this error in their browser (which for now is the only way I know to figure out where tools are *expected* to be): File /home/galaxy/galaxy-dist/tools/rgenetics/rgFastQC.py, line 141, in assert os.path.isfile(opts.executable),'##rgFastQC.py error - cannot find executable %s' % opts.executable AssertionError: ##rgFastQC.py error - cannot find executable /home/galaxy/galaxy-dist/tool-data/shared/jars/FastQC/fastqc Java JARs are a special case, and FastQC has a unique way of locating its jars, which is why it is expected to be found in that directory. This needs to be documented. To fix this I downloaded the FastQC tar file from its webpage, unzipped it, and copied the fastqc binary/script to the home/galaxy/galaxy-dist/tool-data/shared/jars/FastQC/ directory. I also had to mkdir FastQC/ under jars/ to place it there since it didn't already exist. Had I not been told the specific directory by the error I'm not sure how I would have intuitively known to place the binary there (unless I'm overlooking some critical documentation). And how do I know that other similar things are not missing which should be there? Can anyone shed some light on this please? Adding a brief page on the Galaxy wiki site under the Admin section about this would really help, even if it only showed an example for one or two specific tools. The list of external dependencies by tool is maintained here: http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies I'll update this page with links to the new documentation when I write it. I should also add that work is under way to make it possible to automatically install these dependencies as needed. --nate Thanks, Josh ___ 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/ -- Josh Nielsen Systems Administrator HudsonAlpha Institute for Biotechnology 256-319-1485 ___ 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/
Re: [galaxy-dev] How and where to install tool dependencies
Thanks Jeremy, That does clear quite a few things up. I will probably take the route of just adding the directories that contain the tool executables to my path. And I guess I'll just pay attention to which tools are Java based and copy the executables under the jars directory. Thanks for looking on the wiki too. If you find (or create) a suitable wiki page sometime soon would you be so kind as to post a link to it here, for myself and posterity? That would be great. Thanks for your help! P.S. Sorry for the 'double post'. I don't use mailing lists often. -J On Sat, Dec 10, 2011 at 8:33 AM, Jeremy Goecks jeremy.goe...@emory.eduwrote: Josh, It appears that there are shell directories for the tools under ~/galaxy-dist/tools/ with basic wrapper scripts but without the corresponding executables (very few that I've noticed have the tools already in them). Is the intent to download the dependency tools and (building from source if necessary) take the binaries in those directories and copy them to their corresponding directory under ~/galaxy-dist/tools/? This seems to have worked with an error I first got when clipping a FASTQ file which reported that fastx_clipper was not a recognized command. So I downloaded the FASTX Toolkit, compiled the binaries, and copied only the binaries into the corresponding fastx tools directory. Would I do the same thing for TopHat and Cufflinks by taking all their binaries (combined) and copying them into ~/galaxy-dist/tools/ngs_rna/? You'll want to read about Galaxy Tool files a bit to understand the files in ~/galaxy-dist/tools: http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#Admin.2BAC8-Tools.2BAC8-Tool_Config_Syntax.Galaxy_Tool_XML_File These are not shell directories; instead, they include tool config files + additional wrapper scripts to run a tool in Galaxy. To answer your question, executables for tools need to be in your path but do not need to be in the config/wrapper directories. For example, in an SGE cluster, we suggest setting the PATH environment var in ~/.sge_request Even if that is the case though, I have occasionally gotten errors about tools missing in completely different directories. One was for the FASTQ Groomer. One user saw this error in their browser (which for now is the only way I know to figure out where tools are *expected* to be): *File /home/galaxy/galaxy-dist/tools/rgenetics/rgFastQC.py, line 141, in assert os.path.isfile(opts.executable),'##rgFastQC.py error - cannot find executable %s' % opts.executable AssertionError: ##rgFastQC.py error - cannot find executable /home/galaxy/galaxy-dist/tool-data/shared/jars/FastQC/fastqc * The exception to the above is Java-based tools. For these tools, you'll need to use the ~/galaxy-dist/shared/jars directory. This is a limitation of Galaxy that will likely be addressed in the future. Adding a brief page on the Galaxy wiki site under the Admin section about this would really help, even if it only showed an example for one or two specific tools. I looked a bit but couldn't find it; I suspect it is out on the wiki somewhere, though clearly it needs to be easier to find. Good luck, J. -- Josh Nielsen Systems Administrator HudsonAlpha Institute for Biotechnology 256-319-1485 ___ 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/
Re: [galaxy-dev] administrator Interface.
Hi, I have setup a galaxy production server and created a admins.txt file with comma separated account names. When running galaxy and logged into one of the activated accounts I cannot view the interface. Configs Listed Below Cheers James. #Config File file:universe config path:/home/galaxy/galaxy-dist/universe-wsgi. Config line related to the admins folder. admin_users = /home/galaxy/galaxy-dist/tools/SOER1000genes/galaxy/admins.txt #Admin.txt. file:admins.txt path:/home/galaxy/galaxy-dist/tools/SOER1000genes/galaxy/admins.txt #file contents# admin_users=sfk2...@gmail.com ## When I Log in to the account above in galaxy I cannot view the admin interface. I am confused as to what I have done wrong or possibly stupid. ___ 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/
