Re: [galaxy-dev] GalaxyAdmins Group: Future Directions?
Hi Srinivas Thank you very much for e-mail...and thereby reminding me that I haven't replied to Dave's call a week ago. I second most of your thoughts. However, I am not sure of the idea of creating a full-fledged user group with additional opportunities for sharing, learning and collaborating. I like it, but how do you intend to distinguish this group from the current '[galaxy-dev]' group/community? I am afraid stuff will get lost between the two groups or it leads to duplication.probably something we need to discuss in Oslo? I am definitively in favor of a dual leadership - one person from the admin community and one from the Galaxy team. Regards, Hans-Rudolf PS: Do you have stats of who (or how many) has taken part in the past meetups? I think the numbers have been much smaller than the number of responses to Ann's original proposal last April. On 04/05/2013 10:43 PM, Maddhi, Srinivas wrote: Hello, Based on my observations and interactions during the past few meet-ups and as an administrator of Galaxy, the current goals of the group [1] remain relevant and are being met through the meet-ups. An additional benefit to these meet-ups that has evolved is an update from a member of the Galaxy team on upcoming features and other developments. With regard to the future of the group, my suggestion is to keep it going and work towards building a full-fledged user group with additional opportunities for sharing, learning and collaborating. This will strengthen the community, possibly drive increased adoption, and further serve to guide development of Galaxy. Appointing one of more leaders (one each from the Galaxy team and user community) to identify speakers, drive the agenda, set a cadence to the meet-ups and drive the formation of a user group would be helpful, IMHO. Thanks! Notes: 1. Build a community, learn from each other From: Dave Clements cleme...@galaxyproject.org mailto:cleme...@galaxyproject.org Date: Monday, April 1, 2013 11:07 AM To: Galaxy Dev List galaxy-...@bx.psu.edu mailto:galaxy-...@bx.psu.edu Subject: [galaxy-dev] GalaxyAdmins Group: Future Directions? Hello all, The GalaxyAdmins group is coming up on it's one year anniversary (coinciding with GCC2013) and this is a good opportunity to discuss what the future of the group should be. Some starting topics for discussion are on the GalaxyAdmins Future Directions page (http://wiki.galaxyproject.org/Community/GalaxyAdmins/Future). These include * What should the group's goals and activities be? * What type of leadership structure should the group have, and how should it be selected? The discussion, however, is wide open to any topic relevant to the group. If you have any opinions or suggestions please reply to the group. Anyone with an interest in the group is encouraged to post. Once the discussion settles, I will summarize the discussion on the wiki page and suggest an action plan for making those things happen. Thanks, Dave C. -- http://galaxyproject.org/GCC2013 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.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 the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] How to show alert message to user when running a tool in galaxy
On Apr 4, 2013, at 9:41 AM, BingXin Lu wrote: Dear all, I have added a tool in galaxy. After clicking 'Execute', this tool will query an external database for some information to ensure that there are no conflict records in the database. So sometimes an alert message should be sent to user if there are wrong records in the database. But I have not found out an efficient way to implement this in galaxy. I am wondering if it is possible to give some warning message to users when running a tool in galaxy and how to do it if it is feasible. I implemented the tool with an xml file and a python file. I am wondering calling javascript from the python code to give user error information. But it seems infeasible and I do not know where to start. Hi Bingxin, The simplest method would be to output the messages from your tool. For a warning message that does not cause the tool to fail, write the messages to stdout. If the warning conditions should cause the tool to fail, write the messages to stderr. --nate Do you have any ideas? Thank you very much! Best regards, --Bingxin ___ 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] How to show alert message to user when running a tool in galaxy
I will try this method. Thank you very much! 2013/4/8 Nate Coraor n...@bx.psu.edu On Apr 4, 2013, at 9:41 AM, BingXin Lu wrote: Dear all, I have added a tool in galaxy. After clicking 'Execute', this tool will query an external database for some information to ensure that there are no conflict records in the database. So sometimes an alert message should be sent to user if there are wrong records in the database. But I have not found out an efficient way to implement this in galaxy. I am wondering if it is possible to give some warning message to users when running a tool in galaxy and how to do it if it is feasible. I implemented the tool with an xml file and a python file. I am wondering calling javascript from the python code to give user error information. But it seems infeasible and I do not know where to start. Hi Bingxin, The simplest method would be to output the messages from your tool. For a warning message that does not cause the tool to fail, write the messages to stdout. If the warning conditions should cause the tool to fail, write the messages to stderr. --nate Do you have any ideas? Thank you very much! Best regards, --Bingxin ___ 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] REST API: upload of dataset to history possible ?
On Mon, Apr 8, 2013 at 7:58 AM, Marc Logghe marc.log...@ablynx.com wrote: YES!!! I really could not have found that by myself. Thank you very much. Great, I am re-responding to galaxy-dev just in case someone else has this problem. BTW: I have made some additions to blend4j in order to make it compatible to Richard Park's REST API changes regarding the passing of tool parameters. Are these the changes that have made it into Galaxy? If so, if you send me a patch or pull request I would be happy to review it for inclusion into blend4j. Thanks for using blend4j! -John It allows to pass parameters like this: WorkflowInputs inputs = new WorkflowInputs(); inputs.setDestination(new WorkflowInputs.ExistingHistory(history.getId())); inputs.setWorkflowId(projectWorkflow.getId()); // Set parameters for params2yaml tool inputs.setParameters(params2yaml, new ToolParameters(project, APR000200)); Not entirely satisfied with it; might need some api changes but was kind of POC. I also would need some more info from Richard because it is not clear to me if his REST API adjustments allow for multiple parameters. Cheers, Marc -Original Message- From: jmchil...@gmail.com [mailto:jmchil...@gmail.com] On Behalf Of John Chilton Sent: Monday, April 08, 2013 2:50 PM To: Marc Logghe Subject: Re: [galaxy-dev] REST API: upload of dataset to history possible ? Can you retry that with ? as the db key, admittedly that could use some more documentation :). The db key is the short identifier associated with the genome corresponding to the data, ? indicates none is specified. -John On Sun, Apr 7, 2013 at 2:06 PM, Marc Logghe marc.log...@ablynx.com wrote: Thanks John. Not sure what I am doing wrong, but in my hands it does not work. No errors but there is no file upload either. ToolsClient toolsClient = galaxyInstance.getToolsClient(); ClientResponse result = toolsClient.fileUploadRequest(history.getId(), txt, whatIsAdbKey?, new File(C:\\Users\\mlogghe\\Documents\\bb3d562ec52a9fc5.yml)); System.out.println(result.getClientResponseStatus()); In paster.log I also do not see any evidence that upload_handler is called. Regards, Marc -Original Message- From: jmchil...@gmail.com [mailto:jmchil...@gmail.com] On Behalf Of John Chilton Sent: Thursday, April 04, 2013 3:40 PM To: Marc Logghe Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] REST API: upload of dataset to history possible ? On Tue, Apr 2, 2013 at 5:23 AM, Marc Logghe marc.log...@ablynx.com wrote: Hi, Is it currently possible to upload an input dataset to a history via the REST API ? This has been possible since pull request 94: https://bitbucket.org/galaxy/galaxy-central/pull-request/94/enable-upload-of-files-to-history-through/diff. The idea is to use the tools API and to invoke the upload1 tool. I imagine this is a little tricky to do with the bioblend Python library right now, but the blend4j Java library has a high-level helper function (ToolsClient.fileUploadRequest) to make this pretty simple: https://github.com/jmchilton/blend4j/blob/master/src/main/java/com/github/jmchilton/blend4j/galaxy/ToolsClient.java -John Or should one use a library dataset instead ? But in the latter case, only an admin can upload data, right ? Thanks, Marc THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. If the reader of this E-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately at abl...@ablynx.com. Thank you for your co-operation. NANOBODY and NANOCLONE are registered trademarks of Ablynx N.V. ___ 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/ THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. If the reader of this E-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately at abl...@ablynx.com. Thank you for your co-operation. NANOBODY and NANOCLONE are registered trademarks
[galaxy-dev] Galaxy + ProFTPd - proper configuration / uploaded files not accessible in Galaxy
Hi, I am new to Galaxy. I have managed to set up my Galaxy server with PostgreSQL and ProFTPd. I only do not know how to configure the system properly in order to get uploaded files into Galaxy. Problems: 1. I cannot see the files uploaded through ProFTPd from Galaxy. 2. I cannot upload any (even tiny) file through the Galaxy web interface -- Galaxy puts the upload task in the queue and the arrow is blinking (like it is uploading) but it never ends. Problem nr. 1 is solved when I set the current user's home directory access rights to 777. But it does not seem to be the best solution (and the ProFTPd config file shown in http://wiki.galaxyproject.org/Admin/Config/Upload%20via%20FTP is more restrictive than that). I run Galaxy under UNIX user called galaxyuser. And I log into Galaxy as some...@somewhere.com. The access rights on the folders are as follows: drwx--x--x 3 galaxyuser root 4096 dub 5 12:05 /var/ftp_uploads/ /var/ftp_uploads/: total 4 drwx-- 2 65533 65533 4096 dub 8 15:38 some...@somewhere.com I would appreciate any suggestions. Best regards, Jan ___ 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 + ProFTPd - proper configuration / uploaded files not accessible in Galaxy
Hi Jan, you have that line in your config file, right? SQLNamedQuery LookupGalaxyUser SELECT email,password,'1003','1003','/media/data/galaxy_ftp/%U','/bin/bash' FROM galaxy_user WHERE email='%U' 1003 is the group ID of your galaxyuser. Try to adjust that number to your ID. Hope that will work! Bjoern I am new to Galaxy. I have managed to set up my Galaxy server with PostgreSQL and ProFTPd. I only do not know how to configure the system properly in order to get uploaded files into Galaxy. Problems: 1. I cannot see the files uploaded through ProFTPd from Galaxy. 2. I cannot upload any (even tiny) file through the Galaxy web interface -- Galaxy puts the upload task in the queue and the arrow is blinking (like it is uploading) but it never ends. Problem nr. 1 is solved when I set the current user's home directory access rights to 777. But it does not seem to be the best solution (and the ProFTPd config file shown in http://wiki.galaxyproject.org/Admin/Config/Upload%20via%20FTP is more restrictive than that). I run Galaxy under UNIX user called galaxyuser. And I log into Galaxy as some...@somewhere.com. The access rights on the folders are as follows: drwx--x--x 3 galaxyuser root 4096 dub 5 12:05 /var/ftp_uploads/ /var/ftp_uploads/: total 4 drwx-- 2 65533 65533 4096 dub 8 15:38 some...@somewhere.com I would appreciate any suggestions. Best regards, Jan ___ 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/ -- 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Galaxy dont work on my Bio-Linux
On Mar 21, 2013, at 10:19 AM, brozp...@email.cz brozp...@email.cz wrote: Hello, please could you help me, how to run galaxy directly from my computer? I am using Bio-Linux (ubuntu distribution) and there is GALAXY already install. When I try to open it, it is state that: The Galaxy server doesn't seem to be running on your machine. You may need to start it with the command: sudo start galaxy Or else Galaxy may still be starting up (it takes a couple of minutes to get going on the first run). When I open terminal and write sudo start galaxy it is state that galaxy start/running... But when I trying to open galaxy (just double clic on the icon) it still state problem which I write above. Hi Petr, It looks like Upstart believes that Galaxy is running, but Galaxy is not actually listening on the port like it should be. I'd have a look in the Galaxy log file to see whether it's had a problem: /var/log/galaxy/galaxy.log You can also use `sudo restart galaxy` to try restarting the process. --nate Could you help me please how to fix it?? Thank you very much for your reply! Have a nice day, Petr. ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] [cloudbiolinux] Re: Pgp Keys not found error nebc.nerc.ac.uk
Zeeshan and Roman; Thanks for passing this on. The complaints about keys are only warnings so aren't the root cause of the issue. The failure is coming from here: Err http://nebc.nerc.ac.uk unstable Release.gpg Unable to connect to nebc.nerc.ac.uk:http: Zeeshan, it looks like your machine is not able to connect to the Bio-Linux machine for some reason. It might be a transient error if you re-run apt-get update. If not, I'd try to debug either the network or entries in your sources.list. Hope this helps, Brad Zeeshan, wrong mailing list, this really seems like a CloudBiolinux issue, not Galaxy's problem. Sorry for the cross-posting, guys ;__/ The problem lays in here: https://github.com/chapmanb/cloudbiolinux/blob/master/cloudbio/package/deb.py#L52 NEBC GPG keyids do not seem to be there. Cheers! Roman 4 apr 2013 kl. 17:15 skrev Zeeshan Ali Shah zas...@pdc.kth.se: I am getting this when install I tried to serach the following keys on other server but could not find it on other pgp key server Err http://nebc.nerc.ac.uk unstable Release.gpg Unable to connect to nebc.nerc.ac.uk:http: Ign http://nebc.nerc.ac.uk unstable Release Ign http://nebc.nerc.ac.uk unstable/bio-linux TranslationIndex Err http://nebc.nerc.ac.uk unstable/bio-linux amd64 Packages Unable to connect to nebc.nerc.ac.uk:http: Err http://nebc.nerc.ac.uk unstable/bio-linux i386 Packages Unable to connect to nebc.nerc.ac.uk:http: Err http://nebc.nerc.ac.uk unstable/bio-linux Translation-en_US Unable to connect to nebc.nerc.ac.uk:http: Err http://nebc.nerc.ac.uk unstable/bio-linux Translation-en Unable to connect to nebc.nerc.ac.uk:http: Ign http://downloads-distro.mongodb.org dist/10gen Translation-en Fetched 316 B in 3s (99 B/s) W: There is no public key available for the following key IDs: 3B4FE6ACC0B21F32 W: GPG error: http://ppa.launchpad.net precise Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 759A8E0E5BA15160 W: There is no public key available for the following key IDs: 3B4FE6ACC0B21F32 W: There is no public key available for the following key IDs: 3B4FE6ACC0B21F32 W: Failed to fetch http://nebc.nerc.ac.uk/bio-linux/dists/unstable/Release.gpg Unable to connect to nebc.nerc.ac.uk:http: W: Failed to fetch http://nebc.nerc.ac.uk/bio-linux/dists/unstable/bio-linux/binary-amd64/Packages Unable to connect to nebc.nerc.ac.uk:http: W: Failed to fetch http://nebc.nerc.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/Packages Unable to connect to nebc.nerc.ac.uk:http: W: Failed to fetch http://nebc.nerc.ac.uk/bio-linux/dists/unstable/bio-linux/i18n/Translation-en_US Unable to connect to nebc.nerc.ac.uk:http: W: Failed to fetch http://nebc.nerc.ac.uk/bio-linux/dists/unstable/bio-linux/i18n/Translation-en Unable to connect to nebc.nerc.ac.uk:http: -- Regards Zeeshan Ali Shah System Administrator - PDC HPC PhD researcher (IT security) Kungliga Tekniska Hogskolan +46 8 790 9115 http://www.pdc.kth.se/members/zashah ___ 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/ -- You received this message because you are subscribed to the Google Groups cloudbiolinux group. To unsubscribe from this group and stop receiving emails from it, send an email to cloudbiolinux+unsubscr...@googlegroups.com. To post to this group, send email to cloudbioli...@googlegroups.com. Visit this group at http://groups.google.com/group/cloudbiolinux?hl=en. For more options, visit https://groups.google.com/groups/opt_out. ___ 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] April 8, 2013 Galaxy Security Release
A security vulnerability was recently discovered that would allow a malicious
person to delete the contents of a history that does not belong to them. The
vulnerability was in a method designed to allow users to switch between
histories as a convenience from certain messages and is not used for most
normal history switching operations. A fix has been provided in the stable
branch of the Galaxy distribution and tagged as security_2013.04.08.
Administrators are strongly encouraged to upgrade to at least the listed tag or
to implement one of the provided workarounds. This changeset *is not* included
in the most recent (April 1, 2013) stable release.
To upgrade:
% hg pull
% hg update security_2013.04.08
For Galaxy installations on relatively old versions that administrators are not
yet ready to upgrade, there are two workarounds. First, the patch can be
downloaded and applied manually:
% wget -o history.patch
https://bitbucket.org/galaxy/galaxy-central/commits/883216b2eaf2ff05b7771f4ed2541be2ef1ed92f/raw/
and then:
% hg patch history.patch
or:
% patch -p1 history.patch
In this case, the Galaxy server process(es) must be restarted for the change to
take effect.
Second, access to this method via the upstream proxy server can be denied.
Note that anyone with the ability to bypass the proxy server via directly
connecting to the Galaxy application's web port(s) would still be able to call
this method. This is possible for anyone with direct login access to the
server, or even remotely if the Galaxy application binds to all addresses
(instead of just localhost) unless restricted by other means (e.g. a firewall).
For Apache:
Location ~ /history/switch_to_history.*
Deny from all
/Location
For nginx:
location ~ /history/switch_to_history.* {
deny all;
}
If using a proxy prefix (e.g. /galaxy), that prefix should be prepended to
/history.
--nate
Galaxy Team
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Re: [galaxy-dev] History periodically disappears in AWS Cloudman installation
Hello, Greg, If I understand correctly, this may be an error with the server or panel loading the previously-used/most-current history. How many histories are displayed when you use the 'history-options-button' (the gear at the top of the history panel) and click 'Saved Histories'? As a side question, which browser are you using or most commonly using? Thanks for looking, Carl On Fri, Mar 22, 2013 at 8:46 PM, Greg Edwards gedwar...@gmail.com wrote: Hi, We're running a private Cloudman Galaxy on AWS for small-scale proteomics work. Lately the whole History of the main user id we use has occasionally disappeared, ie. on login the History is empty. The datasets aren't hiding in Deleted Datasets. They appear to still be there in /mnt/galaxyData/files/000. They're not in the Anonymous (not logged in ) id. They're not in another id. The data doesn't come back later. We reload the latest datasets in use and the numbering in the history restarts from 1. We're running the most basic config, with the simple single-threaded database. Nothing of interest seems to be in the various Cloudman logs. I've searched the archives for lost/deleted/disappeared datasets/history etc but nothing useful turned up. This is our rev status .. UBUNTU /mnt/galaxyTools/galaxy-central $ hg summary parent: 8116:ecd131b136d0 tip libraries: fix in query for 'datasets_are_public' branch: default commit: 2 modified, 268 unknown update: (current) This is a poor fault report but .. appreciate any pointers here. Many thanks ... -- Greg Edwards, Port Jackson Bioinformatics gedwar...@gmail.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 + ProFTPd - proper configuration / uploaded files not accessible in Galaxy
Hi Björn, yes, this was the problem - I had wrong GID there. Now it works! Thanks! Jan 2013/4/8 Björn Grüning bjoern.gruen...@pharmazie.uni-freiburg.de Hi Jan, you have that line in your config file, right? SQLNamedQuery LookupGalaxyUser SELECT email,password,'1003','1003','/media/data/galaxy_ftp/%U','/bin/bash' FROM galaxy_user WHERE email='%U' 1003 is the group ID of your galaxyuser. Try to adjust that number to your ID. Hope that will work! Bjoern I am new to Galaxy. I have managed to set up my Galaxy server with PostgreSQL and ProFTPd. I only do not know how to configure the system properly in order to get uploaded files into Galaxy. Problems: 1. I cannot see the files uploaded through ProFTPd from Galaxy. 2. I cannot upload any (even tiny) file through the Galaxy web interface -- Galaxy puts the upload task in the queue and the arrow is blinking (like it is uploading) but it never ends. Problem nr. 1 is solved when I set the current user's home directory access rights to 777. But it does not seem to be the best solution (and the ProFTPd config file shown in http://wiki.galaxyproject.org/Admin/Config/Upload%20via%20FTP is more restrictive than that). I run Galaxy under UNIX user called galaxyuser. And I log into Galaxy as some...@somewhere.com. The access rights on the folders are as follows: drwx--x--x 3 galaxyuser root 4096 dub 5 12:05 /var/ftp_uploads/ /var/ftp_uploads/: total 4 drwx-- 2 65533 65533 4096 dub 8 15:38 some...@somewhere.com I would appreciate any suggestions. Best regards, Jan ___ 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/ -- 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] setup grid engine
Hi Jingzhi, Unfortunately, there's a mistake in the sample config for that runner plugin, the line to load the plugin should be: plugin id=drmaa type=runner load=galaxy.jobs.runners.drmaa:DRMAAJobRunner/ The sample config was fixed in a later commit to the stable branch, and seeing as there was a security release today I would suggest just updating your Galaxy installation to the latest stable commit anyway: % hg pull % hg update stable --nate On Apr 8, 2013, at 4:14 PM, Jingzhi Zhu wrote: I have downloaded the 04_01 release and tried to configure the Sun Grid Engine so that the job can run on our cluster. I have export the DRMAA_LIBRARY_PATH environment variable (export DRMAA_LIBRARY_PATH=/home/love-galaxy/bin/libdrmaa.so.1.0). Then copy job_conf.xml.sample_advanced to job_conf.xml. I have deleted some lines on the plugins section so it looks like this in job_conf.xml plugins workers=4 !-- workers is the number of threads for the runner's work queue. The default from plugins is used if not defined for a plugin. -- plugin id=local type=runner load=galaxy.jobs.runners.local:LocalJobRunner/ plugin id=drmaa type=runner load=galaxy.jobs.runners.drmaa:DRMAARunner/ /plugins The run.sh returns the following error galaxy.tools.imp_exp DEBUG 2013-04-08 15:57:12,465 Loaded history export tool: __EXPORT_HISTORY__ galaxy.tools.imp_exp DEBUG 2013-04-08 15:57:12,466 Loaded history import tool: __IMPORT_HISTORY__ galaxy.tools.genome_index DEBUG 2013-04-08 15:57:12,472 Loaded genome index tool: __GENOME_INDEX__ galaxy.jobs.manager DEBUG 2013-04-08 15:57:12,474 Starting job handler galaxy.jobs.runners DEBUG 2013-04-08 15:57:12,475 Starting 4 LocalRunner workers galaxy.jobs DEBUG 2013-04-08 15:57:12,477 Loaded job runner 'galaxy.jobs.runners.local:LocalJobRunner' as 'local' Traceback (most recent call last): File /net/rowley/ifs/data/love/love-galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py, line 37, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File /net/rowley/ifs/data/love/love-galaxy/galaxy-dist/lib/galaxy/app.py, line 159, in __init__ self.job_manager = manager.JobManager( self ) File /net/rowley/ifs/data/love/love-galaxy/galaxy-dist/lib/galaxy/jobs/manager.py, line 31, in __init__ self.job_handler = handler.JobHandler( app ) File /net/rowley/ifs/data/love/love-galaxy/galaxy-dist/lib/galaxy/jobs/handler.py, line 29, in __init__ self.dispatcher = DefaultJobDispatcher( app ) File /net/rowley/ifs/data/love/love-galaxy/galaxy-dist/lib/galaxy/jobs/handler.py, line 543, in __init__ self.job_runners = self.app.job_config.get_job_runner_plugins() File /net/rowley/ifs/data/love/love-galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py, line 476, in get_job_runner_plugins runner_class = getattr( module, class_name ) AttributeError: 'module' object has no attribute 'DRMAARunner' Can someone point to me what is going on here? If you have configured the SGE successfully with the latest 4.1 release, can you show me what the file job_conf.xml should look like? There are a lot of tags in this new XML file and I found it is hard to do it right. Thanks! Jingzhi ___ 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] removing inputs from a pipeline
Philippe, There's not a way to automatically delete intermediate datasets right now, but what you *can* do using workflow outputs is mark them as hidden. An option was recently added to Galaxy to allow the deletion of all hidden datasets in particular history, after which you could purge them all with Purge deleted datasets. Both of these commands should be available in the history menu. -Dannon On Sun, Apr 7, 2013 at 9:06 PM, Philipe Moncuquet philippe.m...@gmail.comwrote: Hi Dev, Is there a way to automatically delete inputs in a pipeline ? Let say you don't want to keep your raw data because of quotas issues and you want your pipeline to do it rather than to do it manually. Regards, Philippe ___ 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] galaxy local installation
Hi,
I was trying to install the galaxy on my laptop and run into the following
error
Some eggs are out of date, attempting to fetch...
Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched
Warning: pycrypto (a dependent egg of Fabric) cannot be fetched
Warning: simplejson (a dependent egg of WebHelpers) cannot be fetched
Fetched http://eggs.galaxyproject.org/ssh/ssh-1.7.14-py2.7.egg
One of Galaxy's managed eggs depends on something which is missing, this is
almost certainly a bug in the egg distribution.
Dependency ssh requires pycrypto=2.1,!=2.4
Traceback (most recent call last):
File ./scripts/fetch_eggs.py, line 37, in module
c.resolve() # Only fetch eggs required by the config
File
/Users/yinan/Course2013Spring/IBOIS58A/galaxy-dist/lib/galaxy/eggs/__init__.py,
line 345, in resolve
egg.resolve()
File
/Users/yinan/Course2013Spring/IBOIS58A/galaxy-dist/lib/galaxy/eggs/__init__.py,
line 168, in resolve
dists = pkg_resources.working_set.resolve( (
self.distribution.as_requirement(), ), env, self.fetch )
File build/bdist.linux-i686/egg/pkg_resources.py, line 569, in resolve
raise VersionConflict(dist,req) # XXX put more info here
pkg_resources.VersionConflict: (ssh 1.7.14
(/Users/yinan/Course2013Spring/IBOIS58A/galaxy-dist/eggs/ssh-1.7.14-py2.7.egg),
Requirement.parse('pycrypto=2.1,!=2.4'))
Fetch failed.
Because I have numpy installed which seems to be conflict to galaxy, so I
was install with virtual python environment (virtualenv), and also tried
the protection environment provided in the galaxy instruction page (
http://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer),
and both came across the same error as indicated above.
Some information you may be interested:
(GalaxyENV)yinan@Macbook galaxy-dist$ python -V
Python 2.7.3
(GalaxyENV)yinan@Macbook galaxy-dist$ python scripts/get_platforms.py
macosx-10.7-x86_64-ucs2
It will be great if you can help me out.
Thanks,
Yinan
--
Yinan Wan, graduate student
Bioinformatics and Genomics program
Huck Institutes of Life Sciences
the Pennsylvania State University
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Re: [galaxy-dev] How to test DRMAA configuration?
It has been a while, but checking in again for any possible solution or advice where to look here? On Tue, Feb 26, 2013 at 10:06 AM, Joshua Orvis jor...@gmail.com wrote: Thanks for your response. That seemed to work, to a point. I redid the same FASTQ-FASTA conversion test and could see using command-line utilities that the job started on the grid (SGE is behind it.) About 10 minutes have gone by though since the job stopped running on the grid and the interface is still spinning as if it's running. I checked the Galaxy log for that job ID and I see these entries: galaxy.jobs.runners.drmaa INFO 2013-02-26 10:51:15,670 (103) queued as 5224332 galaxy.jobs.runners.drmaa DEBUG 2013-02-26 10:51:16,390 (103/5224332) state change: job is queued and active galaxy.jobs.runners.drmaa DEBUG 2013-02-26 10:51:30,422 (103/5224332) state change: job is running galaxy.jobs.runners.drmaa DEBUG 2013-02-26 10:52:32,623 (103/5224332) is still in running state, adding to the DRM queue galaxy.jobs.runners.drmaa DEBUG 2013-02-26 10:54:31,961 (103/5224332) job left DRM queue with following message: code 18: The job specified by the 'jobid' does not exist. The SGE qacct utility for that job shows me that it took 3.5 minutes to run and that the return status was 0, so it executed successfully. It seems that Galaxy is missing the completion event for the job? Joshua On Tue, Feb 26, 2013 at 12:17 AM, Ross ross.laza...@gmail.com wrote: See if adding the default queue name to the job runner path - eg: default_cluster_job_runner = drmaa:///default works any better? Galaxy will default to the local runner if it can't find the nominated drmaa path AFAIK and I don't think 'default' is the default :) On Tue, Feb 26, 2013 at 4:51 PM, Joshua Orvis jor...@gmail.com wrote: I have a working local Galaxy instance and wanted to enable DRMAA support to utilize our SGE (or LSF) grid. Following the guide herehttp://wiki.galaxyproject.org/Admin/Config/Performance/Cluster I set what I appeared to need to make this work. From the DRMAA_LIBRARY_PATH env variable to all the configuration settings in universe_wsgi.ini, reconfiguring the server hosting Galaxy as a submit host, etc. Some specific config file changes made: new_file_path = /seq/gscidA/www/gscid_devel/htdocs/galaxy-dist/database/tmp start_job_runners = drmaa default_cluster_job_runner = drmaa:/// set_metadata_externally = True outputs_to_working_directory = True I then killed and restarted the Galaxy instance and tried a simple FASTQ - FASTA test execution, but it ran locally. I couldn't find any sort of errors or messages related to DRMAA in the server log, and the job ran to completion. I commented out the local tool runner overrides. What can I do to test my DRMAA configuration and where should I look for errors? Thanks - Joshua ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
