Re: [galaxy-dev] Question about compressed files
Hi Ciara, Galaxy supports compressed files like gz [1] by default. Keep in mind that large files like yours are not guaranteed to upload properly, please use other techniques to get your data in galaxy. For example with FTP: http://wiki.g2.bx.psu.edu/FTPUpload Hope that helps, Bjoern [1] .gz/.gzip, .bz/.bzip, .bz2/.bzip2, zip Hi all, My colleague tried to upload via filesystem path a file with an approximate size of 2GB. It was a compressed file (filename.fq.gz). No error was reported, so I thought everything went fine, but when he tried running a tool, the uploaded file did not show in the input dropdown. But when he tried again, this time using an uncompressed file, every thing worked well. Now to my question: by default, can Galaxy accept and use compressed files? Or do I have to change something in its configuration just to do so? Thanks for the help! CL ___ 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/ -- Björn Grüning Albert-Ludwigs-Universität Freiburg Institute of Pharmaceutical Sciences Pharmaceutical Bioinformatics Hermann-Herder-Strasse 9 D-79104 Freiburg i. Br. Tel.: +49 761 203-4872 Fax.: +49 761 203-97769 E-Mail: bjoern.gruen...@pharmazie.uni-freiburg.de Web: http://www.pharmaceutical-bioinformatics.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/
Re: [galaxy-dev] Question about compressed files
Thanks for the quick reply. I've already checked how to configure our Galaxy instance for FTP upload, but due to security reasons, I cannot use that option. I read the wiki for Data Libraries and found that uploading via filesystem path can be used for putting files with size greater than 2GB in Galaxy. Since the data is stored in the same place where our Galaxy is installed, choosing the link option in Upload via Filesystem path seemed good enough. Anyway, at least now I'm sure that Galaxy indeed accepts compressed files. Again, thanks. ___ 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/
[galaxy-dev] Byte-range support for IGV ?
HELLO ! I just updated our local galaxy instance and just wanted to try the new IGV display application. When I try to display a BAM file whith the local IGV, I encounter the following message : HTTP and FTP access to BAM files require byte-range support Has anyone encountred the same probleme? Thanks in advances Regards Amine ___ 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] Liftover tool installation woes
Hello Kwon, Most of this sounds correct. The only issue is with compressed files. Galaxy uses uncompressed liftOver data at our site and this is how we instruct that it be set up (see galaxy-central/tool-data/liftOver.loc.sample). Would you be able to run a test to see if uncompressing resolves the issue? Uncompress one of the over.chain files, modify the .loc file so that the name also reflects the uncompressed naming, then try to use the UI version of liftOver with this uncompressed data. Please let us know how this works out (cc-ing the list, so that others can learn of the confirmed dependency). For now, there is no automated way to enter the .loc data entries. There is some development activity going on right now to address data setup (including liftOver), but nothing is ready yet to be shared. When complete, any new tools will be announced (loudly - we know that they are highly desired). Thanks! Jen Galaxy team On 7/3/12 10:21 PM, Kwon SoonJae wrote: Hi Everyone, I installed a local instance of galaxy and some tools using the command line, and for some reason liftover will work in the command line but won't work in galaxy. Here's what I've done so far: - Downloaded liftover standalone executable from the tool-dependencies page in the Gwiki. - Changed permissions on liftover executable to make it usable in the command prompt (terminal, macosx) - otherwise I get permission denied. - Copied executable over to /usr/local/bin likewise to use in command prompt and in Galaxy. - Modified liftover.loc to include all the conversion types and directories of chain.gz files I downloaded to use with the tool (I believe liftover can make use of both .chain and .chain.gz files). After that I tried to run liftover in Galaxy and it didn't work, giving me some error that said hg19ToMm9 mapping is currently not available. It seems to work fine using the command line though. Since my goal is to setup galaxy locally, I really want to get this working correctly. Can anyone guide me through what's gone wrong? Also, there must be a better way of installing all these tools than manually downloading every single one and using the command line, surely? I had to type out the format of liftover.loc file manually for around 130 chain files... I'm convinced there has to be a better way. Thanks in advance, SJ ___ 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/ -- Jennifer Jackson http://galaxyproject.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/
Re: [galaxy-dev] can not login to workflows after postgresql setup
Hi all, I did manage to log in now after the postgres installation by re-registering. However my workflow is gone. Is there a file stored in galaxy by default which I can reupload to retrieve my workflow?. Also it seems that I am no longer able to upload files. It's only a 300kb test file but it seems to be uploading forever. I'm guessing that some settings need to be adjusted. But I have no clue which ones. Help is very much appreciated! Jaap From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] on behalf of j.w.f.van_der_heij...@lumc.nl [j.w.f.van_der_heij...@lumc.nl] Sent: Wednesday, July 04, 2012 2:29 PM To: bernd.ja...@pasteur.fr; galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] can not login to workflows after postgresql setup Hi all, I have set up postgresql to work with galaxy because the standard mysqlite didn't work with my workflow. Now that postgresql seems to be working I can not login to galaxy. When I try to login it says that it can't find my username. And also when I click forgot password it says: Mail is not configured for this Galaxy instance. Please contact an administrator. Any ideas? Kind Regards Jaap ___ 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] Looking for recommendations: How to run galaxy workflows in batch
In your workflows, are you using Input Dataset steps? Galaxy uses these steps to know how to map datasets to do special things like this. If you're not currently using them, just open the workflow editor and add input dataset steps (it's at the very bottom of the tool list) connected to the tool inputs at the highest level of the workflow, and you'll see the multiple dataset flagging when you go to run it next time. -Dannon On Jul 4, 2012, at 3:19 AM, Bernd Jagla wrote: Dannon Baker dannonbaker@... writes: Hi Dave, Yes, galaxy's standard run-workflow dialog has a feature where you can select multiple datasets as input for a single Input Dataset step. To do this, click the icon referenced by the tooltip in the screenshot below to select multiple files. All parameters remain static between executions except for the single input dataset that gets modified for each run, and that only one input dataset can be set to multiple files in this fashion. -Dannon Dannon, what if I don't have this icon??? How can I enable this? Where is this documented? Thanks, Bernd ___ 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] Question about compressed files
When using the 'upload via filesystem path' option for data libraries, Galaxy will use the file as is without decompressing it. In practice, this means that you'll need to decompress it before uploading it to a library because Galaxy tools expect the dataset to be uncompressed. This is, of course, different behavior than seen when uploading a compressed dataset. In that case, Galaxy will decompress the dataset as needed. Best, J. On Jul 4, 2012, at 5:10 AM, Ciara Ledero wrote: Thanks for the quick reply. I've already checked how to configure our Galaxy instance for FTP upload, but due to security reasons, I cannot use that option. I read the wiki for Data Libraries and found that uploading via filesystem path can be used for putting files with size greater than 2GB in Galaxy. Since the data is stored in the same place where our Galaxy is installed, choosing the link option in Upload via Filesystem path seemed good enough. Anyway, at least now I'm sure that Galaxy indeed accepts compressed files. Again, thanks. ___ 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] can not login to workflows after postgresql setup
I did manage to log in now after the postgres installation by re-registering. However my workflow is gone. Is there a file stored in galaxy by default which I can reupload to retrieve my workflow?. Moving to a new database will make all your previous data inaccessible as it's no longer in the database that Galaxy is using, so this behavior is expected. You could: (a) reconnect Galaxy to your SQLite database and export (download) your workflow and then (b) change Galaxy to use your PostGres database and import (upload) your workflow. Also it seems that I am no longer able to upload files. It's only a 300kb test file but it seems to be uploading forever. The database used should not affect uploading. Are you still having problems? Best, J. ___ 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] Question about compressed files
Thank you for explaining it further, Jeremy. We'll keep that in mind next time we use that method. Anyway, I'm sorry for this redundant post, but I'm getting an error every time I am uploading a file into a data library using my non-admin user account. Galaxy says that there is no valid file within the user directory. The file I am uploading is a .fq file. I've made the necessary changes in universe_wsgi.ini and gave the necessary permissions to my user account. What could be causing that error? Thanks again! CL ___ 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] Liftover tool installation woes
Hi Jen, Thanks for looking into this. I have unzipped all the .gz files so that the directory contains all .chain files. The liftover.loc file has also been modified to refer to all the .chain files instead, as such: http://pastebin.com/xSKGvUtG I still run into the same error if I try to run the tool in Galaxy, though (hg19ToMm9 mapping currently not available). The liftover command still works fine through the command line. I have a feeling the error has to do with the issue with Galaxy's job runner returning anything written to stderr as an error, mentioned here: http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr Seems like it was an issue back in 2010. Has this been rectified? Again, thank you for your help, SJ On Wed, Jul 4, 2012 at 9:42 PM, Jennifer Jackson j...@bx.psu.edu wrote: Hello Kwon, Most of this sounds correct. The only issue is with compressed files. Galaxy uses uncompressed liftOver data at our site and this is how we instruct that it be set up (see galaxy-central/tool-data/liftOver.loc.sample). Would you be able to run a test to see if uncompressing resolves the issue? Uncompress one of the over.chain files, modify the .loc file so that the name also reflects the uncompressed naming, then try to use the UI version of liftOver with this uncompressed data. Please let us know how this works out (cc-ing the list, so that others can learn of the confirmed dependency). For now, there is no automated way to enter the .loc data entries. There is some development activity going on right now to address data setup (including liftOver), but nothing is ready yet to be shared. When complete, any new tools will be announced (loudly - we know that they are highly desired). Thanks! Jen Galaxy team On 7/3/12 10:21 PM, Kwon SoonJae wrote: Hi Everyone, I installed a local instance of galaxy and some tools using the command line, and for some reason liftover will work in the command line but won't work in galaxy. Here's what I've done so far: - Downloaded liftover standalone executable from the tool-dependencies page in the Gwiki. - Changed permissions on liftover executable to make it usable in the command prompt (terminal, macosx) - otherwise I get permission denied. - Copied executable over to /usr/local/bin likewise to use in command prompt and in Galaxy. - Modified liftover.loc to include all the conversion types and directories of chain.gz files I downloaded to use with the tool (I believe liftover can make use of both .chain and .chain.gz files). After that I tried to run liftover in Galaxy and it didn't work, giving me some error that said hg19ToMm9 mapping is currently not available. It seems to work fine using the command line though. Since my goal is to setup galaxy locally, I really want to get this working correctly. Can anyone guide me through what's gone wrong? Also, there must be a better way of installing all these tools than manually downloading every single one and using the command line, surely? I had to type out the format of liftover.loc file manually for around 130 chain files... I'm convinced there has to be a better way. Thanks in advance, SJ ___ 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/ -- Jennifer Jacksonhttp://galaxyproject.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/
[galaxy-dev] conflicting migration files
When I merged brad chapmans code into galaxy-central two 0099 migration files are created. I got things working by moving the ngs lims one to 0104 , but now i think i'll be in for a problem when a new 104 is created... What's the right way to solve this? Brad -- Brad Langhorst langho...@neb.commailto:langho...@neb.com 978-380-7564 ___ 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/
