Re: [galaxy-dev] Strange behaviour with galaxy history
Hi Carl, Thank you for your quite extensive answer! I finally managed to find the line in universe_wsgi.ini that caused the problem. The moment I UNCOMMENT the following line: #log_actions = True I no longer can see the histories. The moment I comment this line again everything works fine. Anyway, this exercise resulted in a clean and updated universe_wsgi.ini file and the problem is solved now! Thank you for your help! Regards, Dr. Philip de Groot Ph.D. Bioinformatics Researcher Wageningen University / TIFN Nutrigenomics Consortium Nutrition, Metabolism Genomics Group Division of Human Nutrition PO Box 8129, 6700 EV Wageningen Visiting Address: Erfelijkheidsleer: De Valk, Building 304 Dreijenweg 2, 6703 HA Wageningen Room: 0052a T: +31-317-485786 F: +31-317-483342 E-mail: philip.degr...@wur.nlmailto:philip.degr...@wur.nl Internet: http://www.nutrigenomicsconsortium.nl http://humannutrition.wur.nl/ https://madmax.bioinformatics.nl/ From: Carl Eberhard [carlfeberh...@gmail.com] Sent: 11 July 2013 16:34 To: Groot, Philip de Cc: galaxy-dev@lists.bx.psu.edu; ambrose.andong...@rothamsted.ac.uk Subject: Re: Strange behaviour with galaxy history Hello, Phillip I haven't been able to replicate this yet (https://trello.com/c/LdLlJDo9). Do you see any errors in your log near or after GET /history/list HTTP/1.1? Shane Sturrock worked around this problem by updating his universe_wsgi.ini file (if I understand his procedure): 1. Make a backup of your universe_wsgi.ini file (for example, copy it to your home directory) 2. Rename the universe_wsgi.ini file in your galaxy installation something like 'universe_wsgi.ini.saved' 3. Rename the most recent universe_wsgi.ini.sample file (that came with the latest update) to universe_wsgi.ini. 4. Copy any custom settings for your server from your older universe_wsgi.ini.saved file to the newer universe_wsgi.ini file 5. Start Galaxy That seemed to work for Shane. Ambrose re-installed and reconnected his database. Neither is a solution to the original cause, but you may want to try them while we investigate. Thanks, Carl On Thu, Jul 11, 2013 at 5:48 AM, Groot, Philip de philip.degr...@wur.nlmailto:philip.degr...@wur.nl wrote: Hi, First of all, I apologize for interrupting into this discussion, but I have exactly the same problem and did not find a solution yet. And no: prefix and cookies are set properly in our particular setting (as /)! This is not the cause... I think that the problem occurred with the May Galaxy update, but it was unnoticed for a while. Problem is that the histories of all users are not listed when being asked for it within Galaxy. Only the current history is present for every user. In addition, when I login using another computer, a different history is being depicted (which suggest a cookie issue but I just cannot find it). Copying the current history works but the copy is not listed either. In the postgres database, the histories are properly listed. If I type in the proper history name in Galaxy, I even get the stored history back! So this all works, but users cannot see their histories. The java console does not reveal any problem. prefix and cookie are set properly (I think). So I don't know. Does anyone have any clue on how to tackle this issue? I am happy to provide more information if needed! Thanks! Dr. Philip de Groot Ph.D. Bioinformatics Researcher Wageningen University / TIFN Nutrigenomics Consortium Nutrition, Metabolism Genomics Group Division of Human Nutrition PO Box 8129, 6700 EV Wageningen Visiting Address: Erfelijkheidsleer: De Valk, Building 304 Dreijenweg 2, 6703 HA Wageningen Room: 0052a T: +31-317-485786tel:%2B31-317-485786 F: +31-317-483342tel:%2B31-317-483342 E-mail: philip.degr...@wur.nlmailto:philip.degr...@wur.nlmailto:philip.degr...@wur.nlmailto:philip.degr...@wur.nl Internet: http://www.nutrigenomicsconsortium.nlhttp://www.nutrigenomicsconsortium.nl/ http://humannutrition.wur.nl/ https://madmax.bioinformatics.nl/ ___ 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/
Re: [galaxy-dev] Strange behaviour with galaxy history
Many thanks for the observation. This will come handy next time I hit the same rock. I hope not so soon. Ambrose -Original Message- From: Groot, Philip de [mailto:philip.degr...@wur.nl] Sent: 16 July 2013 12:03 To: Carl Eberhard Cc: galaxy-dev@lists.bx.psu.edu; Ambrose Andongabo (RRes-Roth) Subject: RE: Strange behaviour with galaxy history Hi Carl, Thank you for your quite extensive answer! I finally managed to find the line in universe_wsgi.ini that caused the problem. The moment I UNCOMMENT the following line: #log_actions = True I no longer can see the histories. The moment I comment this line again everything works fine. Anyway, this exercise resulted in a clean and updated universe_wsgi.ini file and the problem is solved now! Thank you for your help! Regards, Dr. Philip de Groot Ph.D. Bioinformatics Researcher Wageningen University / TIFN Nutrigenomics Consortium Nutrition, Metabolism Genomics Group Division of Human Nutrition PO Box 8129, 6700 EV Wageningen Visiting Address: Erfelijkheidsleer: De Valk, Building 304 Dreijenweg 2, 6703 HA Wageningen Room: 0052a T: +31-317-485786 F: +31-317-483342 E-mail: philip.degr...@wur.nlmailto:philip.degr...@wur.nl Internet: http://www.nutrigenomicsconsortium.nl http://humannutrition.wur.nl/ https://madmax.bioinformatics.nl/ From: Carl Eberhard [carlfeberh...@gmail.com] Sent: 11 July 2013 16:34 To: Groot, Philip de Cc: galaxy-dev@lists.bx.psu.edu; ambrose.andong...@rothamsted.ac.uk Subject: Re: Strange behaviour with galaxy history Hello, Phillip I haven't been able to replicate this yet (https://trello.com/c/LdLlJDo9). Do you see any errors in your log near or after GET /history/list HTTP/1.1? Shane Sturrock worked around this problem by updating his universe_wsgi.ini file (if I understand his procedure): 1. Make a backup of your universe_wsgi.ini file (for example, copy it to your home directory) 2. Rename the universe_wsgi.ini file in your galaxy installation something like 'universe_wsgi.ini.saved' 3. Rename the most recent universe_wsgi.ini.sample file (that came with the latest update) to universe_wsgi.ini. 4. Copy any custom settings for your server from your older universe_wsgi.ini.saved file to the newer universe_wsgi.ini file 5. Start Galaxy That seemed to work for Shane. Ambrose re-installed and reconnected his database. Neither is a solution to the original cause, but you may want to try them while we investigate. Thanks, Carl On Thu, Jul 11, 2013 at 5:48 AM, Groot, Philip de philip.degr...@wur.nlmailto:philip.degr...@wur.nl wrote: Hi, First of all, I apologize for interrupting into this discussion, but I have exactly the same problem and did not find a solution yet. And no: prefix and cookies are set properly in our particular setting (as /)! This is not the cause... I think that the problem occurred with the May Galaxy update, but it was unnoticed for a while. Problem is that the histories of all users are not listed when being asked for it within Galaxy. Only the current history is present for every user. In addition, when I login using another computer, a different history is being depicted (which suggest a cookie issue but I just cannot find it). Copying the current history works but the copy is not listed either. In the postgres database, the histories are properly listed. If I type in the proper history name in Galaxy, I even get the stored history back! So this all works, but users cannot see their histories. The java console does not reveal any problem. prefix and cookie are set properly (I think). So I don't know. Does anyone have any clue on how to tackle this issue? I am happy to provide more information if needed! Thanks! Dr. Philip de Groot Ph.D. Bioinformatics Researcher Wageningen University / TIFN Nutrigenomics Consortium Nutrition, Metabolism Genomics Group Division of Human Nutrition PO Box 8129, 6700 EV Wageningen Visiting Address: Erfelijkheidsleer: De Valk, Building 304 Dreijenweg 2, 6703 HA Wageningen Room: 0052a T: +31-317-485786tel:%2B31-317-485786 F: +31-317-483342tel:%2B31-317-483342 E-mail: philip.degr...@wur.nlmailto:philip.degr...@wur.nlmailto:philip.degr...@wur.nlmailto:philip.degr...@wur.nl Internet: http://www.nutrigenomicsconsortium.nlhttp://www.nutrigenomicsconsortium.nl/ http://humannutrition.wur.nl/ https://madmax.bioinformatics.nl/ -- This message has been scanned for viruses and dangerous content by MailScanner, and we believe but do not warrant that this e-mail and any attachments thereto do not contain any viruses. However, you are fully responsible for performing any virus scanning. -- This message has been scanned for viruses and dangerous content by MailScanner, and we believe but do not warrant that this e-mail and any attachments thereto do not contain any viruses. However, you are fully responsible for performing any virus
[galaxy-dev] repeat tag enhancement?
Hey guys, i was searching the mailing list and wiki for some hints if there is a possibility to enhance the repeat tag. We want to give the option to our users to add more than one additional set of the contained parameters at one go e.g. 10 or 20 or 50, because it can be very frustrating to click the add new dataset button 50 times. Is there any option to do this with a text field or preset like add 20 new datasets or something like that? I would be very thankful for an advice. Greetings, Thomas ___ 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/
Re: [galaxy-dev] Testing with repeat parameters
Oops, I was replying via theGalaxy Development List Archive http://dev.list.galaxyproject.org/ interface, strange it has put the reply off list... So no functional test for my tool ( despite my enthousiasm :-) ), since the repeat tags must be provided in the test. Thanks, Joachim. Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team On 07/16/2013 01:46 PM, Peter Cock wrote: Off list? They don't work yet, bar the simplest case of 0 or 1 repeats using a single parameter perhaps. Peter On Tuesday, July 16, 2013, wrote: Hi Peter, I was wondering if you have details on how to include tests for repeat tag sets? Cheers, Joachim quote author='Peter Cock' Hello all, Should unit tests with repeat parameters work? If so, how do I give each repeat group in the XML for the test? Sample tool here: http://testtoolshed.g2.bx.psu.edu/view/peterjc/venn_list inputs param name=main_lab size=30 type=text value=Venn Diagram label=Plot title/ conditional name=universe param name=type_select type=select label=Implicit or explicit full ID list? option value=explicitExplicit/option option value=implicitImplicit (use union of sets below)/option /param when value=explicit param name=main type=data format=tabular,fasta,fastq,sff label=Full dataset (with all identifiers) help=Tabular file (uses column one), FASTA, FASTQ or SFF file./ /when when value=implicit/ /conditional repeat name=sets min=1 max=3 title=Sets param name=set type=data format=tabular,fasta,fastq,sff label=Members of set help=Tabular file (uses column one), FASTA, FASTQ or SFF file./ param name=lab size=30 type=text value=Group label=Caption for set/ /repeat /inputs The first test attempts to use the repeat set/lab once - guessing at how to give repeat parameters in a test: test param name=type_select value=explicit/ param name=main value=venn_list.tabular ftype=tabular/ param name=main_lab value=Some Proteins/ param name=set value=rhodopsin_proteins.fasta/ param name=lab value=Rhodopsins/ output name=PDF file=venn_list1.pdf ftype=pdf/ /test $ ./run_functional_tests.sh -id venn_list ... python /mnt/galaxy/galaxy-central/tools/plotting/venn_list.py /mnt/galaxy/galaxy-central/database/files/000/dataset_1.dat tabular Some Proteins /mnt/galaxy/galaxy-central/database/files/000/dataset_2.dat fasta Rhodopsins /mnt/galaxy/galaxy-central/database/files/000/dataset_2.dat fasta Group /mnt/galaxy/galaxy-central/database/files/000/dataset_3.dat ... This seems to have resulted in two repeat entries, and so fails. What I was expecting was: python /mnt/galaxy/galaxy-central/tools/plotting/venn_list.py /mnt/galaxy/galaxy-central/database/files/000/dataset_1.dat tabular Some Proteins /mnt/galaxy/galaxy-central/database/files/000/dataset_2.dat fasta Rhodopsins /mnt/galaxy/galaxy-central/database/files/000/dataset_3.dat Thanks, 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ /quote Quoted from: http://dev.list.galaxyproject.org/Testing-with-repeat-parameters-tp4659840.html _ Sent from http://dev.list.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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Testing with repeat parameters
OK, it seems that the current state of the functional test framework 'simulates' one click on the 'repeat' button. You just provide one set of param names contained within the repeat block. Luckily, this is enough for my tool now. Cheers, Joachim Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team On 07/16/2013 01:49 PM, Joachim Jacob | VIB | wrote: Oops, I was replying via theGalaxy Development List Archive http://dev.list.galaxyproject.org/ interface, strange it has put the reply off list... So no functional test for my tool ( despite my enthousiasm :-) ), since the repeat tags must be provided in the test. Thanks, Joachim. Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team On 07/16/2013 01:46 PM, Peter Cock wrote: Off list? They don't work yet, bar the simplest case of 0 or 1 repeats using a single parameter perhaps. Peter On Tuesday, July 16, 2013, wrote: Hi Peter, I was wondering if you have details on how to include tests for repeat tag sets? Cheers, Joachim quote author='Peter Cock' Hello all, Should unit tests with repeat parameters work? If so, how do I give each repeat group in the XML for the test? Sample tool here: http://testtoolshed.g2.bx.psu.edu/view/peterjc/venn_list inputs param name=main_lab size=30 type=text value=Venn Diagram label=Plot title/ conditional name=universe param name=type_select type=select label=Implicit or explicit full ID list? option value=explicitExplicit/option option value=implicitImplicit (use union of sets below)/option /param when value=explicit param name=main type=data format=tabular,fasta,fastq,sff label=Full dataset (with all identifiers) help=Tabular file (uses column one), FASTA, FASTQ or SFF file./ /when when value=implicit/ /conditional repeat name=sets min=1 max=3 title=Sets param name=set type=data format=tabular,fasta,fastq,sff label=Members of set help=Tabular file (uses column one), FASTA, FASTQ or SFF file./ param name=lab size=30 type=text value=Group label=Caption for set/ /repeat /inputs The first test attempts to use the repeat set/lab once - guessing at how to give repeat parameters in a test: test param name=type_select value=explicit/ param name=main value=venn_list.tabular ftype=tabular/ param name=main_lab value=Some Proteins/ param name=set value=rhodopsin_proteins.fasta/ param name=lab value=Rhodopsins/ output name=PDF file=venn_list1.pdf ftype=pdf/ /test $ ./run_functional_tests.sh -id venn_list ... python /mnt/galaxy/galaxy-central/tools/plotting/venn_list.py /mnt/galaxy/galaxy-central/database/files/000/dataset_1.dat tabular Some Proteins /mnt/galaxy/galaxy-central/database/files/000/dataset_2.dat fasta Rhodopsins /mnt/galaxy/galaxy-central/database/files/000/dataset_2.dat fasta Group /mnt/galaxy/galaxy-central/database/files/000/dataset_3.dat ... This seems to have resulted in two repeat entries, and so fails. What I was expecting was: python /mnt/galaxy/galaxy-central/tools/plotting/venn_list.py /mnt/galaxy/galaxy-central/database/files/000/dataset_1.dat tabular Some Proteins /mnt/galaxy/galaxy-central/database/files/000/dataset_2.dat fasta Rhodopsins /mnt/galaxy/galaxy-central/database/files/000/dataset_3.dat Thanks, 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ /quote Quoted from: http://dev.list.galaxyproject.org/Testing-with-repeat-parameters-tp4659840.html _ Sent from http://dev.list.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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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
[galaxy-dev] provide group(s) association as a tool parameter
Hi there! Is there an easy way to pass a users group associations to a tool as a parameter. Maybe similar to pass user information via the reserved variable $__user_email__ ?! I tried $__app__.model.UserGroupAssociation.group however I end up with a mapper-object and are kind of stuck here... Thnx, Christian ___ 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/
[galaxy-dev] Galaxy Local Admin user
Dear Madam/Sir, I have installed Galaxy Local in our system. I registered as a user. However when I try to give admin status to some users, I am unable despite following the steps mentioned in the help. To give a user Galaxy admin privileges, add their Galaxy login ( email ) to the list in the following config setting in the Galaxy configuration file universe_wsgi.ini. # this should be a comma-separated list of valid Galaxy users admin_users = us...@bx.psu.edu,us...@bx.psu.edu I have done what is mentioned above and the universe_wsgi.ini is edited accordingly. Still when I log on to Galaxy Local I don't see the admin tab. Can you kindly help me. With warmest regards Chadi EL Farran (Post Graduate Student) Dr. Jonathan Yuin-Han Loh's Laboratory #08-01, Institute of Molecular and Cell Biology (IMCB) 61 Biopolis Drive, Proteos Singapore 138673 Contact No: +65-91944793 E-mail: ch...@nus.edu.sg ___ 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/
Re: [galaxy-dev] Galaxy Local Admin user
Hi Just double checking: Have you restarted Galaxy? Regards, Hans-Rudolf On 07/16/2013 07:23 AM, Chadi Abdul Kader El Farran wrote: Dear Madam/Sir, I have installed Galaxy Local in our system. I registered as a user. However when I try to give admin status to some users, I am unable despite following the steps mentioned in the help. To give a user Galaxy admin privileges, add their Galaxy login ( email ) to the list in the following config setting in the Galaxy configuration file universe_wsgi.ini. # this should be a comma-separated list of valid Galaxy users admin_users = us...@bx.psu.edu,us...@bx.psu.edu I have done what is mentioned above and the universe_wsgi.ini is edited accordingly. Still when I log on to Galaxy Local I don't see the admin tab. Can you kindly help me. With warmest regards Chadi EL Farran (Post Graduate Student) Dr. Jonathan Yuin-Han Loh's Laboratory #08-01, Institute of Molecular and Cell Biology (IMCB) 61 Biopolis Drive, Proteos Singapore 138673 Contact No: +65-91944793 E-mail: ch...@nus.edu.sg ___ 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/ ___ 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/
Re: [galaxy-dev] [galaxy-user] Connecting to new Galaxy Cloudman by FTP
Hey Mo, You can use ssh to connect to the Galaxy machine. If you used cloudlaunch to create your instance, it should display an example connection string that will work from e.g. a linux/mac shell, something like: 'ssh -i cloudman_keypair.pem ubuntu@IP', after your instance launched. Once inside of the machine, you can do something like: 'sudo -iu galaxy', to switch to the galaxy user and then have a look at the mount points under /mnt/. The cloudman_keypair.pem file is the key file that you (should have) downloaded the first time that you launched a cloudman instance, or when you manually generated a keypair. You can create additional keypairs in your aws console if you need to download a new one to use (you can probably delete the existing cloudman_keypair and have it regenerated automatically by cloudman, but I haven't tested this and I wouldn't recommend doing this if an instance is running). You'll need to use the correct .pem file for the keypair that you specified during launch of the instance. See http://docs.aws.amazon.com/AWSEC2/latest/UserGuide/generating-a-keypair.html for Amazon's info on creating keypairs (especially if you are using e.g. Windows and putty: http://docs.aws.amazon.com/AWSEC2/latest/UserGuide/putty.html). Once you make the changes to the files locally, you can use the Cloudman Admin web UI to restart the Galaxy instance. Let us know if you encounter any issues. Thanks for using Galaxy, Dan On Jul 15, 2013, at 7:22 PM, Mohammad Heydarian wrote: Hey Nate, Thanks for the response and instructions. I understand the last three steps of your protocol, but the first step is difficult for me to understand. I'm guessing that, 1. Set 'use_pbkdf2 = False' in universe_wsgi.ini anywhere in the [app:main] section, is telling me to change a setting of Cloudman by command line. This is generally where we get stuck in using Cloudman, because we aren't familiar with command line (we get cold sweats and light palpitations) and are weary of making changes to the Cloudman code. I would ask our IT guys for help, but their expertise ends at updating Office tools. I would bother a programmer or bioinformatician, but most of them are so busy you need a formal collaboration to get on their radar. I would ask people who vaguely know command line for help, but most of the time their knowledge of command line is just higher than mine and we end up troubleshooting an issue neither of us can really grasp. So, is there a webcast, or video, or slideshow, that can show a newbie how to command line into Cloudman and make the changes you outline in step 1? Cheers, Mo Heydarian On Mon, Jul 15, 2013 at 4:22 PM, Nate Coraor n...@bx.psu.edu wrote: On Jul 8, 2013, at 3:50 PM, Mohammad Heydarian wrote: Hi, I am having trouble setting up a FTP connection with the recently released version of Galaxy Cloudman (ami-118bfc78). I have instantiated the new version of Galaxy Cloudman with CloudLaunch and also through the AWS EC2 wizard (using the same security group settings as the previous versions) and neither instance will connect to my FTP connection. Has anyone else had this problem? Does anyone know what is preventing the FTP connection? Any help would be greatly appreciated. Hey Mo, This may be a case of the new password hashing algorithm's incompatibility with the provided ProFTPD config. Could you try the following: 1. Set 'use_pbkdf2 = False' in universe_wsgi.ini anywhere in the [app:main] section 2. Restart Galaxy 3. Reset your password in the Galaxy UI 4. Test FTP again --nate Cheers, Mo Heydarian ___ 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/ ___ 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/ ___ 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
Re: [galaxy-dev] repeat tag enhancement?
I like your proposal. I don't think it is currently possible to add - say - 5 repeat blocks at once. Feel free to add and describe your suggested enhancement on Trello, so I can vote for it :-) http://galaxyproject.org/trello Cheers, Joachim Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team On 07/16/2013 01:34 PM, Berner, Thomas wrote: Hey guys, i was searching the mailing list and wiki for some hints if there is a possibility to enhance the repeat tag. We want to give the option to our users to add more than one additional set of the contained parameters at one go e.g. 10 or 20 or 50, because it can be very frustrating to click the “add new dataset” button 50 times. Is there any option to do this with a text field or preset like “add 20 new datasets” or something like that? I would be very thankful for an advice. Greetings, Thomas ___ 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/ ___ 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/
Re: [galaxy-dev] repeat tag enhancement?
Rather than adding additional increments to add/remove, what about allowing the user to directly set the number of elements in the repeat? -- James Taylor, Assistant Professor, Biology/CS, Emory University On Tue, Jul 16, 2013 at 7:34 AM, Berner, Thomas thomas.ber...@jki.bund.de wrote: Hey guys, i was searching the mailing list and wiki for some hints if there is a possibility to enhance the repeat tag. We want to give the option to our users to add more than one additional set of the contained parameters at one go e.g. 10 or 20 or 50, because it can be very frustrating to click the “add new dataset” button 50 times. Is there any option to do this with a text field or preset like “add 20 new datasets” or something like that? I would be very thankful for an advice. Greetings, Thomas ___ 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/ ___ 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/
[galaxy-dev] Cloudman database issue (?)
Hello, I found a couple of issues in using the latest version of Cloudman (revision:10201:ebe87051fadf). The Extract Genomic DNA tool returns an error: No sequences are available for 'mm9', request them by reporting this error. Upon trying to report the error in Galaxy (on the page that comes up when you click the bug icon) I get the error: Mail is not configured for this galaxy instance Any help on fixing the Extract Genomic DNA tool would be great. Thanks. Cheers, Mo Heydarian ___ 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/
Re: [galaxy-dev] Cloudman database issue (?)
Hey Mo, The new volume we pushed out for the conference has several known issues. Enis and I are both away from the office on travel right now, but updating the volume and fixing these issues is the first thing I'll be doing when I'm back next week. For now, you can launch using the pre-conference AMI and cloudman bucket using something like https://main.g2.bx.psu.edu/cloudlaunch?ami=ami-da58aab3bucket_default=gxy-workshop -Dannon On Tue, Jul 16, 2013 at 12:24 PM, Mohammad Heydarian mheyd...@jhmi.eduwrote: Hello, I found a couple of issues in using the latest version of Cloudman (revision:10201:ebe87051fadf). The Extract Genomic DNA tool returns an error: No sequences are available for 'mm9', request them by reporting this error. Upon trying to report the error in Galaxy (on the page that comes up when you click the bug icon) I get the error: Mail is not configured for this galaxy instance Any help on fixing the Extract Genomic DNA tool would be great. Thanks. Cheers, Mo Heydarian ___ 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/ ___ 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/
Re: [galaxy-dev] To move galaxy local Production Instance to a new server setup
Dear All, We have had a working local galaxy instance being used with mySQL for almost two years with a lot of new scripts, workflows built-in and datasets still associated with it. We now would like to move to a new server but rather than start from scratch, would like to move all parts of current instance as is first. We ran deploy_galaxy.sh of galaxy-admin-utils-master, modifying hg clone to point to our current instance. As it copied the virtual environment details also, I expected to be able to run start_galaxy.sh without requiring new eggs to be compiled. Where did I go wrong. Is it always required to re-compile them? Or is there a way to copy the missing eggs. Please advise. Error last few lines: Traceback (most recent call last): File ./scripts/fetch_eggs.py, line 37, in module c.resolve() # Only fetch eggs required by the config File /home/ocimum/GalaxyMigrated/galaxy-dist/lib/galaxy/eggs/__init__.py, line 345, in resolve egg.resolve() File /home/ocimum/GalaxyMigrated/galaxy-dist/lib/galaxy/eggs/__init__.py, line 195, in resolve return self.version_conflict( e.args[0], e.args[1] ) File /home/ocimum/GalaxyMigrated/galaxy-dist/lib/galaxy/eggs/__init__.py, line 226, in version_conflict r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg.fetch ) File /home/ocimum/GalaxyMigrated/galaxy_venv/local/lib/python2.7/site-packages/distribute-0.6.24-py2.7.egg/pkg_resources.py, line 584, in resolve raise DistributionNotFound(req) pkg_resources.DistributionNotFound: numpy==1.6.0 Fetch failed. Regards, Madhuri This e-mail contains PRIVILEGED AND CONFIDENTIAL INFORMATION intended solely for the use of the addressee(s). If you are not the intended recipient, please notify the sender by e-mail and delete the original message. Further, you are not to copy, disclose, or distribute this e-mail or its contents to any other person and any such actions that are unlawful. This e-mail may contain viruses. Ocimum Biosolutions has taken every reasonable precaution to minimize this risk, but is not liable for any damage you may sustain as a result of any virus in this e-mail. You should carry out your own virus checks before opening the e-mail or attachment. The information contained in this email and any attachments is confidential and may be subject to copyright or other intellectual property protection. If you are not the intended recipient, you are not authorized to use or disclose this information, and we request that you notify us by reply mail or telephone and delete the original message from your mail system. OCIMUMBIO SOLUTIONS (P) LTD___ 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/
Re: [galaxy-dev] DRMAA Runner URL Specify TORQUE host
I've had success using the pbs runner rather than drmaa runner for this case. It's quite straightforward to specify the pbs_server for the pbs runner. Works just as the documentation indicates. - Bart On Tue, Jul 9, 2013 at 1:46 PM, Bart Gottschalk bgott...@umn.edu wrote: I haven't been able to find a way to make the drmaa runner work in this situation. I'm going to move on to trying this with a pbs runner instead. I will post to this thread if this works for me. - Bart ___ 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/
Re: [galaxy-dev] CloudMan Error
Thanks guys! I'm going to try it out now.
Would you mind letting me know when the issues are fixed next week?
(updating this thread would be fine)
Thanks again,
Greg
On Tue, Jul 16, 2013 at 12:42 PM, Dannon Baker dannon.ba...@gmail.com wrote:
Hey Greg,
We put together a quick workaround until we're able to resolve the
underlying issues. You can launch the previous incarnation of galaxy
(pre-update AMI and Cloudman versions) using
https://main.g2.bx.psu.edu/cloudlaunch?ami=ami-da58aab3bucket_default=gxy-workshop
Once your instance is up, enter your share string like usual and it'll work
fine. We expect to fix these issues next week, but this should get your
instance back up and running for now.
On Mon, Jul 15, 2013 at 10:19 AM, greg margeem...@gmail.com wrote:
Thanks for getting back to me, Enis.
I went ahead and started a new cluster instance. I'll try to leave it
running today in case there's anything we want to check.
Here's my whole process:
Start Screen Setup:
--
http://snag.gy/DMIeC.jpg
Entering my share string:
http://snag.gy/wKFLy.jpg
Main Page Text and log:
Cluster name:
MSGGREG
Disk status:
0 / 0 (0%)
Worker status:
Idle: 0 Available: 0 Requested: 0
Service status:
Applications
Data
Cluster status log
14:08:32 - Master starting
14:08:34 - Completed the initial cluster startup process. This is a
new cluster; waiting to configure the type.
14:08:50 - Migration service prerequisites OK; starting the service
14:08:50 - SGE service prerequisites OK; starting the service
14:08:58 - Setting up SGE...
14:09:13 - HTCondor service prerequisites OK; starting the service
14:09:21 - Hadoop service prerequisites OK; starting the service
14:09:38 - Done adding Hadoop service; service running.
14:11:53 - Error creating volume from shared cluster's snapshot
'['snap-cfa775ba']': 'filesystems'
Admin Page CloudMan Log: (unfortunately nothing is jumping out at me?)
---
CloudMan from Galaxy
Admin | Report bugs | Wiki | Screencast
The entire log file (paster.log) is shown. Show latest | Back to admin
view
Python version: (2, 7)
Image configuration suports: {'apps': ['cloudman', 'galaxy']}
2013-07-15 14:08:32,406 DEBUGapp:68 Initializing app
2013-07-15 14:08:32,407 DEBUGec2:121 Gathering instance
zone, attempt 0
2013-07-15 14:08:32,410 DEBUGec2:127 Instance zone is
'us-east-1d'
2013-07-15 14:08:32,410 DEBUGec2:45 Gathering instance
ami, attempt 0
2013-07-15 14:08:32,412 DEBUGapp:71 Running on 'ec2'
type of cloud in zone 'us-east-1d' using image 'ami-118bfc78'.
2013-07-15 14:08:32,412 DEBUGapp:89 Getting pd.yaml
2013-07-15 14:08:32,412 DEBUGec2:338 No S3 Connection,
creating a new one.
2013-07-15 14:08:32,413 DEBUGec2:342 Got boto S3 connection.
2013-07-15 14:08:32,452 DEBUG misc:212 Checking if bucket
'cm-0479bd75a331acc874033e98b2e1e03e' exists... it does not.
2013-07-15 14:08:32,452 DEBUG misc:583 Bucket
'cm-0479bd75a331acc874033e98b2e1e03e' does not exist, did not get
remote file 'persistent_data.yaml'
2013-07-15 14:08:32,452 DEBUGapp:96 Setting
deployment_version to 2
2013-07-15 14:08:32,453 INFO app:103 Master starting
2013-07-15 14:08:32,453 DEBUG master:55 Initializing console
manager - cluster start time: 2013-07-15 14:08:32.453182
2013-07-15 14:08:32,453 DEBUG comm:42 AMQP Connection
Failure: [Errno 111] Connection refused
2013-07-15 14:08:32,453 DEBUG master:791 Trying to discover
any worker instances associated with this cluster...
2013-07-15 14:08:32,454 DEBUGec2:317 Establishing boto
EC2 connection
2013-07-15 14:08:32,535 DEBUGec2:305 Got region as
'RegionInfo:us-east-1'
2013-07-15 14:08:32,777 DEBUGec2:326 Got boto EC2
connection for region 'us-east-1'
2013-07-15 14:08:33,022 DEBUG misc:574 Retrieved file
'snaps.yaml' from bucket 'cloudman' on host 's3.amazonaws.com' to
'cm_snaps.yaml'.
2013-07-15 14:08:33,035 DEBUGec2:286 Got region name as
'us-east-1'
2013-07-15 14:08:33,035 DEBUG master:226 Loaded default
snapshot data: [{'snap_id': 'snap-adad90fc', 'name': 'galaxy',
'roles': 'galaxyTools,galaxyData'}, {'snap_id': 'snap-5b030634',
'name': 'galaxyIndices', 'roles': 'galaxyIndices'}]
2013-07-15 14:08:33,035 DEBUGec2:81 Gathering instance
id, attempt 0
2013-07-15 14:08:33,037 DEBUGec2:87 Instance ID is
'i-5346d733'
2013-07-15 14:08:33,125 DEBUGec2:360 Adding tag
'clusterName:MSGGREG' to resource 'i-5346d733'
2013-07-15 14:08:33,307 DEBUGec2:360 Adding tag
'role:master' to resource 'i-5346d733'
2013-07-15
[galaxy-dev] Plugins
Are there any plans in the works to support plugins within Galaxy? One of the tools I'm working on is actually more of an extension of the workflow canvas/editor's user interface. Right now, I've minimized the modifications required to the editor.mako file to simply adding a mako include near the bottom of the file. However, like I just said, this requires editing a Galaxy file. It would be a lot better if Galaxy supported plugins with hooks, thus allowing me to extend the user interface (or any other part of the application) by registering hooks in a plugin. To demonstrate how easy it would be to integrate plugins into a python application, I've written up a simple plugin manager script (~100 loc) an placed it in a gist: https://gist.github.com/mepcotterell/6004997. Using this (or something similar to this) would make Galaxy extremely extensible. The only hard part would be figuring out where you want to place the hooks and documenting them for plugin developers. Sincerely, Michael E. Cotterell Ph.D. Student in Computer Science, University of Georgia Instructor of Record, Graduate RA TA, University of Georgia Faculty Liaison, CS Graduate Student Association, University of Georgia mepcotter...@gmail.com (mailto:mepcotter...@gmail.com) mepc...@uga.edu (mailto:mepc...@uga.edu) m...@cs.uga.edu (mailto:m...@cs.uga.edu) http://michaelcotterell.com/ ___ 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/
Re: [galaxy-dev] Plugins
James, That's exactly what I was thinking. In my opinion, hooks are the way to go (as seen in my example), but if there's a better way then I'm game for that to. I just want to be able to extend Galaxy without modifying Galaxy itself. Thanks! Sincerely, Michael E. Cotterell Ph.D. Student in Computer Science, University of Georgia Instructor of Record, Graduate RA TA, University of Georgia Faculty Liaison, CS Graduate Student Association, University of Georgia mepcotter...@gmail.com (mailto:mepcotter...@gmail.com) mepc...@uga.edu (mailto:mepc...@uga.edu) m...@cs.uga.edu (mailto:m...@cs.uga.edu) http://michaelcotterell.com/ On Tuesday, July 16, 2013 at 2:05 PM, James Taylor wrote: Michael, Galaxy is all about plugins! Tools, datatypes, batch systems, visualizations, et cetera. Additional ways to extend Galaxy through plugins are very welcome. We just need to make sure that whatever solution is chosen is extremely general. -- James Taylor, Assistant Professor, Biology/CS, Emory University On Tue, Jul 16, 2013 at 1:57 PM, Michael E. Cotterell mepcotter...@gmail.com (mailto:mepcotter...@gmail.com) wrote: Are there any plans in the works to support plugins within Galaxy? One of the tools I'm working on is actually more of an extension of the workflow canvas/editor's user interface. Right now, I've minimized the modifications required to the editor.mako file to simply adding a mako include near the bottom of the file. However, like I just said, this requires editing a Galaxy file. It would be a lot better if Galaxy supported plugins with hooks, thus allowing me to extend the user interface (or any other part of the application) by registering hooks in a plugin. To demonstrate how easy it would be to integrate plugins into a python application, I've written up a simple plugin manager script (~100 loc) an placed it in a gist: https://gist.github.com/mepcotterell/6004997. Using this (or something similar to this) would make Galaxy extremely extensible. The only hard part would be figuring out where you want to place the hooks and documenting them for plugin developers. Sincerely, Michael E. Cotterell Ph.D. Student in Computer Science, University of Georgia Instructor of Record, Graduate RA TA, University of Georgia Faculty Liaison, CS Graduate Student Association, University of Georgia mepcotter...@gmail.com (mailto:mepcotter...@gmail.com) mepc...@uga.edu (mailto:mepc...@uga.edu) m...@cs.uga.edu (mailto:m...@cs.uga.edu) http://michaelcotterell.com/ ___ 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/ ___ 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/
Re: [galaxy-dev] Plugins
Michael, Galaxy is all about plugins! Tools, datatypes, batch systems, visualizations, et cetera. Additional ways to extend Galaxy through plugins are very welcome. We just need to make sure that whatever solution is chosen is extremely general. -- James Taylor, Assistant Professor, Biology/CS, Emory University On Tue, Jul 16, 2013 at 1:57 PM, Michael E. Cotterell mepcotter...@gmail.com wrote: Are there any plans in the works to support plugins within Galaxy? One of the tools I'm working on is actually more of an extension of the workflow canvas/editor's user interface. Right now, I've minimized the modifications required to the editor.mako file to simply adding a mako include near the bottom of the file. However, like I just said, this requires editing a Galaxy file. It would be a lot better if Galaxy supported plugins with hooks, thus allowing me to extend the user interface (or any other part of the application) by registering hooks in a plugin. To demonstrate how easy it would be to integrate plugins into a python application, I've written up a simple plugin manager script (~100 loc) an placed it in a gist: https://gist.github.com/mepcotterell/6004997. Using this (or something similar to this) would make Galaxy extremely extensible. The only hard part would be figuring out where you want to place the hooks and documenting them for plugin developers. Sincerely, Michael E. Cotterell Ph.D. Student in Computer Science, University of Georgia Instructor of Record, Graduate RA TA, University of Georgia Faculty Liaison, CS Graduate Student Association, University of Georgia mepcotter...@gmail.com (mailto:mepcotter...@gmail.com) mepc...@uga.edu (mailto:mepc...@uga.edu) m...@cs.uga.edu (mailto:m...@cs.uga.edu) http://michaelcotterell.com/ ___ 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/ ___ 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/
Re: [galaxy-dev] Galaxy-less Tool Installing
On Mon, Jul 15, 2013 at 7:27 PM, John Chilton chil...@msi.umn.edu wrote: One of my goals for the GCC was to sell the idea that tool shed repositories need to be installable without a database present. I John, as I've mentioned in the past I'm very strongly in favor of this. There is absolutely no reason why the ToolShed needs to be tied to Galaxy. For dependency installation we've now got a nice system that does version isolation well, and I've had several groups express interest in using the wrappers from the ToolShed in environments other than Galaxy. from Greg and others (Dave, Bjorn, Peter, Nate) has gone into building a modular dependency system that could very easily be leveraged by applications other than Galaxy, so the extra steps that could be taken to make this possible should to make the codebase as broadly useful and to encourage adoption. Exactly! 1. Rework installing tool shed repositories to not require a database. A kind of messy way to do this might be adding a use_database flag throughout. A cleaner way might be to use allow the core functionality to work with callbacks or plugins that performed the database interactions. Personally I would definitely prefer a plugin model. Basically, a layer isolating the underlying datastore used during tool installation, dependency resolution, et cetera. However, it occurs to me that even if the tool installation component is isolation from Galaxy, it could still use the same model and database. All package management systems need some way to maintain state, a sqlite database is not an unreasonable choice. 2. Separate the core functionality out of the Galaxy code base entirely into a reusable, stand-alone library. This is a long term goal for us. I think at first we'd like to at least see it all happen in the same repository so that we can still support a checkout and run scenario. But decoupling the various web applications and share components that make up the Galaxy ecosystem is very important. include building a little tool shed version of the module command - http://linux.die.net/man/1/module to demonstrate this work and have something immediately useful produced. YES! Absolutely. One of the reasons for the way tool dependency injection was implemented was to support a command line module system. Coupling this with the toolshed to also enable dependency installation and management completes the puzzle. (and yes to all the various commands, through I figured it would be gx_module ;) This would be different from using the API scripts because there would be no API, Galaxy instance, or Galaxy database involved - just the Galaxy code. If this was able to split into its own Python library, one could imagine even allowing something like tsmodule to be installable right from pip and recursively fetch a toolshed_client library or something like that. Absolutely. ___ 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/
[galaxy-dev] BWA Illumina Mapping / BWA Reference Genome
Hello Ladies and Gentlemen, I am Moritz Juchler from University Heidelberg. For my Bachelor thesis I have to choose a bioinformatic pipeline management tool to find SNP's in genomes from hcc patients. My decision was made in favor of galaxy. I have a 64-bit openSuse 11.3 server. I have installed Galaxy locally, since we have a) very large files (30GB per patient) and b) the data is protection sensitive. I kept close to http://wiki.galaxyproject.org/Admin/Get%20Galaxy Now I would like to run this bpipe pipeline: http://pastebin.com/sZd5vfdL And the first step is to align my genome to a *hg19 reference genome* which I have locally under /genedata/human_genome_GRCh37/. trr@portalmoritz:~ ls -l /genedata/human_genome_GRCh37/ total 8486312 -rw-r--r-- 1 trr root 3199905909 2013-06-25 16:44 hg19.fa -rw-r--r-- 1 trr root 8591 2013-07-01 16:06 hg19.fa.amb -rw-r--r-- 1 trr root 4040 2013-07-01 16:06 hg19.fa.ann -rw-r--r-- 1 trr root 3137161344 2013-07-01 16:05 hg19.fa.bwt -rw-r--r-- 1 trr root 784290318 2013-07-01 16:06 hg19.fa.pac -rw-r--r-- 1 trr root 1568580688 2013-07-01 16:31 hg19.fa.sa *bwa is installed and gives me:* trr@portalmoritz:~ bwa Program: bwa (alignment via Burrows-Wheeler transformation) Version: 0.7.5a-r405 Contact: Heng Li l...@sanger.ac.uk Then I tried to follow this guide: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup to get the reference files and http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies. This is my *$PATH* trr@portalmoritz:~ echo $PATH /home/trr/bin:/usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/X11R6/bin:/usr/games:/home/trr/bpipe-0.9.8/bin:/home/trr/bwa-0.7.5a:/home/trr/samtools-0.1.19 *In the universe_wsgi.ini I changed:* tool_dependency_dir = /home/trr/galaxy-dist/tool_dependency_dir debug = False use_interactive = True library_import_dir = /genedata/ allow_library_path_paste = True admin_users = ... This is my *tool_dependency_dir:* trr@portalmoritz:~/galaxy-dist/tool_dependency_dir/bwa ls -l total 4 drwxr-xr-x 3 trr users 4096 2013-07-16 14:28 0.7.4 lrwxrwxrwx 1 trr users6 2013-07-16 14:17 default - 0.7.4/ This is the* version folder of bwa:* trr@portalmoritz:~/galaxy-dist/tool_dependency_dir/bwa/0.7.4 ls -l total 8 drwxr-xr-x 2 trr users 4096 2013-07-16 14:18 bin -rw-r--r-- 1 trr users 47 2013-07-16 14:22 env.sh This is the *content of env.sh:* trr@portalmoritz:~/galaxy-dist/tool_dependency_dir/bwa/0.7.4 cat env.sh PATH=/home/trr/bwa-0.7.5a/:$PATH export PATH And this is the *content of the bin folder:* trr@portalmoritz:~/galaxy-dist/tool_dependency_dir/bwa/0.7.4/bin ls -l total 3896 -rw-r--r-- 1 trr users 6098 2013-07-16 14:18 bamlite.c -rw-r--r-- 1 trr users 3124 2013-07-16 14:18 bamlite.h -rw-r--r-- 1 trr users 24816 2013-07-16 14:18 bamlite.o -rw-r--r-- 1 trr users 11508 2013-07-16 14:18 bntseq.c -rw-r--r-- 1 trr users 2557 2013-07-16 14:18 bntseq.h -rw-r--r-- 1 trr users 37440 2013-07-16 14:18 bntseq.o -rwxr-xr-x 1 trr users 998217 2013-07-16 14:18 bwa -rw-r--r-- 1 trr users 24225 2013-07-16 14:18 bwa.1 -rw-r--r-- 1 trr users 9416 2013-07-16 14:18 bwa.c -rw-r--r-- 1 trr users 1381 2013-07-16 14:18 bwa.h I got the xmls and .py from https://bitbucket.org/galaxy/galaxy-dist/src/da9d740fce31/tools/sr_mapping and i didnt change them at all and put them into ~/galaxy-dist/*tools/sr_mapping * (since they were missing in this folder) bwa_color_wrapper.xml bwa_wrapper.py bwa_wrapper.xml I added *bwa_index_color.loc and bwa_index.loc* to ~galaxy-dist/*tool-data* (they were missing as well, there* were no* bwa_index_color.loc.sample or bwa_index.lox.sample files!!!) I only have this single line in both bwa_index_color.loc and bwa_index.loc trr@portalmoritz:~/galaxy-dist/tool-data cat bwa_index_color.loc #This is a sample file distributed with Galaxy that enables tools # #unique_build_id dbkey display_name file_path hg19hg19hg19/genedata/human_genome_GRCh37/hg19.fa (Spaces are actually tabs!) After all that, I neither have the Map with BWA for Illuminahttps://main.g2.bx.psu.edu/tool_runner?tool_id=toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3 in my local Galaxy version, nor do I find the reference genome. If i missed on any required, please tell me, I will answer you as soon as possible. Sincerly Yours Moritz Juchler ___ 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/
[galaxy-dev] Galaxy ego fetching error (Mac OS X 10.8)
Hi Team, I am attempting to rebuild my local instance of galaxy on my Mac since having been upgraded to Mountain Lion. I have installed Mercurial, postgres, python2.7. I have cloned the latest galaxy-dist. However, when I attempted to launch galaxy with sh run.sh it fails to complete the fetch. Here is what I get: milkyway:galaxy-dist itw$ sh run.sh Initializing datatypes_conf.xml from datatypes_conf.xml.sample Initializing external_service_types_conf.xml from external_service_types_conf.xml.sample Initializing migrated_tools_conf.xml from migrated_tools_conf.xml.sample Initializing reports_wsgi.ini from reports_wsgi.ini.sample Initializing shed_tool_conf.xml from shed_tool_conf.xml.sample Initializing tool_conf.xml from tool_conf.xml.sample Initializing shed_tool_data_table_conf.xml from shed_tool_data_table_conf.xml.sample Initializing tool_data_table_conf.xml from tool_data_table_conf.xml.sample Initializing tool_sheds_conf.xml from tool_sheds_conf.xml.sample Initializing data_manager_conf.xml from data_manager_conf.xml.sample Initializing shed_data_manager_conf.xml from shed_data_manager_conf.xml.sample Initializing openid_conf.xml from openid_conf.xml.sample Initializing universe_wsgi.ini from universe_wsgi.ini.sample Initializing tool-data/shared/ncbi/builds.txt from builds.txt.sample Initializing tool-data/shared/ensembl/builds.txt from builds.txt.sample Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample Initializing tool-data/shared/ucsc/publicbuilds.txt from publicbuilds.txt.sample Initializing tool-data/shared/igv/igv_build_sites.txt from igv_build_sites.txt.sample Initializing tool-data/shared/rviewer/rviewer_build_sites.txt from rviewer_build_sites.txt.sample Initializing tool-data/add_scores.loc from add_scores.loc.sample Initializing tool-data/alignseq.loc from alignseq.loc.sample Initializing tool-data/all_fasta.loc from all_fasta.loc.sample Initializing tool-data/annotation_profiler_options.xml from annotation_profiler_options.xml.sample Initializing tool-data/annotation_profiler_valid_builds.txt from annotation_profiler_valid_builds.txt.sample Initializing tool-data/bfast_indexes.loc from bfast_indexes.loc.sample Initializing tool-data/binned_scores.loc from binned_scores.loc.sample Initializing tool-data/blastdb.loc from blastdb.loc.sample Initializing tool-data/blastdb_p.loc from blastdb_p.loc.sample Initializing tool-data/bowtie2_indices.loc from bowtie2_indices.loc.sample Initializing tool-data/ccat_configurations.loc from ccat_configurations.loc.sample Initializing tool-data/codingSnps.loc from codingSnps.loc.sample Initializing tool-data/encode_datasets.loc from encode_datasets.loc.sample Initializing tool-data/faseq.loc from faseq.loc.sample Initializing tool-data/funDo.loc from funDo.loc.sample Initializing tool-data/gatk_annotations.txt from gatk_annotations.txt.sample Initializing tool-data/gatk_sorted_picard_index.loc from gatk_sorted_picard_index.loc.sample Initializing tool-data/liftOver.loc from liftOver.loc.sample Initializing tool-data/maf_index.loc from maf_index.loc.sample Initializing tool-data/maf_pairwise.loc from maf_pairwise.loc.sample Initializing tool-data/microbial_data.loc from microbial_data.loc.sample Initializing tool-data/mosaik_index.loc from mosaik_index.loc.sample Initializing tool-data/ngs_sim_fasta.loc from ngs_sim_fasta.loc.sample Initializing tool-data/perm_base_index.loc from perm_base_index.loc.sample Initializing tool-data/perm_color_index.loc from perm_color_index.loc.sample Initializing tool-data/phastOdds.loc from phastOdds.loc.sample Initializing tool-data/picard_index.loc from picard_index.loc.sample Initializing tool-data/quality_scores.loc from quality_scores.loc.sample Initializing tool-data/regions.loc from regions.loc.sample Initializing tool-data/sam_fa_indices.loc from sam_fa_indices.loc.sample Initializing tool-data/sam_fa_new_indices.loc from sam_fa_new_indices.loc.sample Initializing tool-data/sequence_index_base.loc from sequence_index_base.loc.sample Initializing tool-data/sequence_index_color.loc from sequence_index_color.loc.sample Initializing tool-data/sift_db.loc from sift_db.loc.sample Initializing tool-data/srma_index.loc from srma_index.loc.sample Initializing tool-data/twobit.loc from twobit.loc.sample Initializing static/welcome.html from welcome.html.sample Some eggs are out of date, attempting to fetch... Fetched http://eggs.galaxyproject.org/Mako/Mako-0.4.1-py2.7.egg Fetched http://eggs.galaxyproject.org/Fabric/Fabric-1.4.2-py2.7.egg Fetched http://eggs.galaxyproject.org/Babel/Babel-0.9.4-py2.7.egg Fetched http://eggs.galaxyproject.org/Whoosh/Whoosh-0.3.18-py2.7.egg Fetched http://eggs.galaxyproject.org/Parsley/Parsley-1.1-py2.7.egg Fetched http://eggs.galaxyproject.org/lrucache/lrucache-0.2-py2.7.egg Fetched http://eggs.galaxyproject.org/sqlalchemy_migrate/sqlalchemy_migrate-0.7.2-py2.7.egg Fetched http://eggs.galaxyproject.org/NoseHTML/NoseHTML-0.4.1-py2.7.egg Fetched
[galaxy-dev] toolshed repository down?
Hi.
Getting error when trying to install the latest Galaxy on a new stand alone
linux RH server. Is the repository down?
migrate.versioning.repository DEBUG 2013-07-16 14:14:46,235 Config:
{'db_settings': {'__name__': 'db_settings', 'required_dbs': '[]',
'version_table': 'migrate_tools', 'repository_id': '
GalaxyTools'}}
tool_shed.galaxy_install.migrate.check DEBUG 2013-07-16 14:14:46,240
psycopg2 egg successfully loaded for postgres dialect
The URL
http://toolshed.g2.bx.psu.edu/repository/get_tool_dependencies?name=bowtie_wrappersowner=devteamchangeset_revision=0c7e4eadfb3cfrom_install_manager=True
raised the exception:
urlopen error [Errno 110] Connection timed out
The URL
http://toolshed.g2.bx.psu.edu/repository/get_tool_dependencies?name=bowtie_color_wrappersowner=devteamchangeset_revision=fd0914e451c5from_install_manager=True
raised the exception:
urlopen error [Errno 110] Connection timed out
The URL
http://toolshed.g2.bx.psu.edu/repository/get_tool_dependencies?name=lastzowner=devteamchangeset_revision=0801f8207d30from_install_manager=True
raised the exception:
urlopen error [Errno 110] Connection timed out
The URL
http://toolshed.g2.bx.psu.edu/repository/get_tool_dependencies?name=lastz_paired_readsowner=devteamchangeset_revision=96825cee5c25from_install_manager=True
raised the exception:
urlopen error [Errno 110] Connection timed out
Traceback (most recent call last):
...
return tool_shed_accessible, missing_tool_configs_dict
UnboundLocalError: local variable 'missing_tool_configs_dict' referenced
before assignment
Regards,
Linda___
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/
Re: [galaxy-dev] Strange behaviour with galaxy history
Nice catch! I'll see where this leads. On Tue, Jul 16, 2013 at 7:03 AM, Groot, Philip de philip.degr...@wur.nlwrote: Hi Carl, Thank you for your quite extensive answer! I finally managed to find the line in universe_wsgi.ini that caused the problem. The moment I UNCOMMENT the following line: #log_actions = True I no longer can see the histories. The moment I comment this line again everything works fine. Anyway, this exercise resulted in a clean and updated universe_wsgi.ini file and the problem is solved now! Thank you for your help! Regards, Dr. Philip de Groot Ph.D. Bioinformatics Researcher Wageningen University / TIFN Nutrigenomics Consortium Nutrition, Metabolism Genomics Group Division of Human Nutrition PO Box 8129, 6700 EV Wageningen Visiting Address: Erfelijkheidsleer: De Valk, Building 304 Dreijenweg 2, 6703 HA Wageningen Room: 0052a T: +31-317-485786 F: +31-317-483342 E-mail: philip.degr...@wur.nlmailto:philip.degr...@wur.nl Internet: http://www.nutrigenomicsconsortium.nl http://humannutrition.wur.nl/ https://madmax.bioinformatics.nl/ From: Carl Eberhard [carlfeberh...@gmail.com] Sent: 11 July 2013 16:34 To: Groot, Philip de Cc: galaxy-dev@lists.bx.psu.edu; ambrose.andong...@rothamsted.ac.uk Subject: Re: Strange behaviour with galaxy history Hello, Phillip I haven't been able to replicate this yet (https://trello.com/c/LdLlJDo9). Do you see any errors in your log near or after GET /history/list HTTP/1.1? Shane Sturrock worked around this problem by updating his universe_wsgi.ini file (if I understand his procedure): 1. Make a backup of your universe_wsgi.ini file (for example, copy it to your home directory) 2. Rename the universe_wsgi.ini file in your galaxy installation something like 'universe_wsgi.ini.saved' 3. Rename the most recent universe_wsgi.ini.sample file (that came with the latest update) to universe_wsgi.ini. 4. Copy any custom settings for your server from your older universe_wsgi.ini.saved file to the newer universe_wsgi.ini file 5. Start Galaxy That seemed to work for Shane. Ambrose re-installed and reconnected his database. Neither is a solution to the original cause, but you may want to try them while we investigate. Thanks, Carl On Thu, Jul 11, 2013 at 5:48 AM, Groot, Philip de philip.degr...@wur.nl mailto:philip.degr...@wur.nl wrote: Hi, First of all, I apologize for interrupting into this discussion, but I have exactly the same problem and did not find a solution yet. And no: prefix and cookies are set properly in our particular setting (as /)! This is not the cause... I think that the problem occurred with the May Galaxy update, but it was unnoticed for a while. Problem is that the histories of all users are not listed when being asked for it within Galaxy. Only the current history is present for every user. In addition, when I login using another computer, a different history is being depicted (which suggest a cookie issue but I just cannot find it). Copying the current history works but the copy is not listed either. In the postgres database, the histories are properly listed. If I type in the proper history name in Galaxy, I even get the stored history back! So this all works, but users cannot see their histories. The java console does not reveal any problem. prefix and cookie are set properly (I think). So I don't know. Does anyone have any clue on how to tackle this issue? I am happy to provide more information if needed! Thanks! Dr. Philip de Groot Ph.D. Bioinformatics Researcher Wageningen University / TIFN Nutrigenomics Consortium Nutrition, Metabolism Genomics Group Division of Human Nutrition PO Box 8129, 6700 EV Wageningen Visiting Address: Erfelijkheidsleer: De Valk, Building 304 Dreijenweg 2, 6703 HA Wageningen Room: 0052a T: +31-317-485786tel:%2B31-317-485786 F: +31-317-483342tel:%2B31-317-483342 E-mail: philip.degr...@wur.nlmailto:philip.degr...@wur.nlmailto: philip.degr...@wur.nlmailto:philip.degr...@wur.nl Internet: http://www.nutrigenomicsconsortium.nl http://www.nutrigenomicsconsortium.nl/ http://humannutrition.wur.nl/ https://madmax.bioinformatics.nl/ ___ 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/
Re: [galaxy-dev] Galaxy-less Tool Installing
On Tue, Jul 16, 2013 at 1:16 PM, James Taylor ja...@jamestaylor.org wrote: On Mon, Jul 15, 2013 at 7:27 PM, John Chilton chil...@msi.umn.edu wrote: One of my goals for the GCC was to sell the idea that tool shed repositories need to be installable without a database present. I John, as I've mentioned in the past I'm very strongly in favor of this. There is absolutely no reason why the ToolShed needs to be tied to Galaxy. For dependency installation we've now got a nice system that does version isolation well, and I've had several groups express interest in using the wrappers from the ToolShed in environments other than Galaxy. from Greg and others (Dave, Bjorn, Peter, Nate) has gone into building a modular dependency system that could very easily be leveraged by applications other than Galaxy, so the extra steps that could be taken to make this possible should to make the codebase as broadly useful and to encourage adoption. Exactly! 1. Rework installing tool shed repositories to not require a database. A kind of messy way to do this might be adding a use_database flag throughout. A cleaner way might be to use allow the core functionality to work with callbacks or plugins that performed the database interactions. Personally I would definitely prefer a plugin model. Basically, a layer isolating the underlying datastore used during tool installation, dependency resolution, et cetera. However, it occurs to me that even if the tool installation component is isolation from Galaxy, it could still use the same model and database. All package management systems need some way to maintain state, a sqlite database is not an unreasonable choice. An sqlite database wasn't what I was imaging, but it seems thoroughly reasonable and the cleanest thing to implement. 2. Separate the core functionality out of the Galaxy code base entirely into a reusable, stand-alone library. This is a long term goal for us. I think at first we'd like to at least see it all happen in the same repository so that we can still support a checkout and run scenario. But decoupling the various web applications and share components that make up the Galaxy ecosystem is very important. Agreed. include building a little tool shed version of the module command - http://linux.die.net/man/1/module to demonstrate this work and have something immediately useful produced. YES! Absolutely. One of the reasons for the way tool dependency injection was implemented was to support a command line module system. Coupling this with the toolshed to also enable dependency installation and management completes the puzzle. (and yes to all the various commands, through I figured it would be gx_module ;) This would be different from using the API scripts because there would be no API, Galaxy instance, or Galaxy database involved - just the Galaxy code. If this was able to split into its own Python library, one could imagine even allowing something like tsmodule to be installable right from pip and recursively fetch a toolshed_client library or something like that. Absolutely. ___ 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/
