[galaxy-dev] Configuring Galaxy for FTP upload
Hi all, According to Galaxy, uploading files larger than 2GB will surely fail. For this reason, uploading via FTP is recommended. Unfortunately, I cannot download/install an FTP server for Galaxy since I am working on a remote server. I only have access to it via Xming. Is there anyway to allow FTP upload, without using ProFTPd? Can I use Mozilla's fireFTP or Linux's own FTP? (Actually, I tried to connect to Galaxy, but I was denied access.). Thank you in advance for any help. CL ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] putting up a SNP module on galaxy
Hi Xiangyu, This question is best directed to the galaxy development list, which I've cc'd. In general, to integrate a tool into Galaxy, you'll want to write a tool wrapper: http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax and then upload it to the Galaxy toolshed: http://wiki.g2.bx.psu.edu/Tool%20Shed You can also upload workflows to the tool shed as well: http://wiki.g2.bx.psu.edu/Tool%20Shed#Enabling_workflow_sharing:_importing_a_workflow_via_a_URL Feel free to email the galaxy-dev list with any questions you may have. Best, J. On Apr 23, 2012, at 3:51 PM, Deng, Xiangyu (CDC/OID/NCEZID) (CTR) wrote: > Hi Jeremy, > > My name is Xiangyu, working across street at the enteric disease laboratory > branch, CDC. I built a SNP calling pipeline and want to put it somewhere with > a friendly GUI so our/other wet lab persons can use it. I wonder if I can do > it on Galaxy. > > The pipeline, written in python, uses bowtie 2, samtools, velvet, biopython > and a perl program. > > Thanks, > Xiangyu > > --- > Xiang-yu Deng, Ph.D. > > ASM Fellow > Enteric Diseases Laboratory Branch > Division of Foodborne, Waterborne and Environmental Diseases > National Center for Emerging and Zoonotic Infectious Diseases > Centers for Disease Control and Prevention > MS-C03, 1600 Clifton Road, Atlanta, GA 30333 > Office: 404-639-1036 > de...@cdc.gov > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Galaxy does not generate consistent results
I used bwa to align a short read file to a reference sequence. I ran it several times, and I got different results for the runs on the same input dataset. The fist run, it generated a ~280,000 lines "gzipped file". I checked the file on the server, and it was actually a sam file, not gzipped. The second run, it generated ~90,000 lines sam file. The third run, it generated ~130,000 lines sam file. The fourth run, it generated ~220,000 lines "gzipped file" Does anyone meet the similar problem? Thank you very much. Cai ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Galaxy with postgresql
Hi Greg, I commented out sqlite line, but I missed "database_connection = " in the new line I added in the configuration file. It is working now. Thank you very much for the quick reply. Cai --- 12年4月24日，周二, Greg Von Kuster 写道： 发件人: Greg Von Kuster 主题: Re: [galaxy-dev] Galaxy with postgresql 收件人: "zhengqiu cai" 抄送: galaxy-dev@lists.bx.psu.edu 日期: 2012年4月24日,周二,上午2:08 Hi Cal, Did you comment out this line? # By default, Galaxy uses a SQLite database found here #database_file = database/universe.sqlite Also, I assume you following reference: in Galaxy configuration file, use postgresql postgres:///galaxy_db?user=ubuntu&host=/var/run/postgresql actually looks like this in your config file: database_connection = postgres:///galaxy_db?user=ubuntu&host=/var/run/postgresql Greg Von Kuster On Apr 23, 2012, at 2:03 PM, zhengqiu cai wrote: Hi All, I want to use postgresql instead of sqlite, and below is how I did the settings: I am running Galaxy under the user ubuntu, so first I create the ubuntu user sudo -u postgres createuser -D -A -P ubuntu Then I create the database named galaxy_db sudo -u postgres createdb -O ubuntu galaxy_db in Galaxy configuration file, use postgresql postgres:///galaxy_db?user=ubuntu&host=/var/run/postgresql When I start Galaxy, sqlite dialect, not postgresql is selected. I am pasting part of the log below: galaxy.model.migrate.check DEBUG 2012-04-23 17:59:52,676 pysqlite>=2 egg successfully loaded for sqlite dialect galaxy.model.migrate.check INFO 2012-04-23 17:59:52,707 At database version 93 galaxy.tool_shed.migrate.check DEBUG 2012-04-23 17:59:52,718 pysqlite>=2 egg successfully loaded for sqlite dialect galaxy.tool_shed.migrate.check INFO 2012-04-23 17:59:52,730 At migrate_tools version 1 galaxy.model.custom_types DEBUG 2012-04-23 17:59:52,735 pysqlite>=2 egg successfully loaded for sqlite dialect Is there anything wrong with my configuration? Thank you. Cai ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] JobManager object has no attribute dispatcher
On Apr 19, 2012, at 11:12 AM, Nate Coraor wrote: > On Apr 19, 2012, at 10:44 AM, Peter Cock wrote: > >> On Thu, Apr 19, 2012 at 2:53 PM, Nate Coraor wrote: >>> On Apr 17, 2012, at 9:04 AM, Peter Cock wrote: >>> Hi all, Does anyone know what might have introduced this problem running galaxy-dist when using the task splitting functionality? I'm using the latest code from the default branch, changeset: 7027:f6e790d94282 >>> >>> Hi Peter, >>> >>> This was resolved in changeset 5c93ac32ace1. Thanks for reporting it. >>> >>> --nate >> >> Are you sure? I've just updated to the tip and the same problem >> persists. Also looking at that commit it isn't obvious how is might >> be linked to this issue: >> https://bitbucket.org/galaxy/galaxy-central/changeset/5c93ac32ace1 > > You're right, that's what I get for reading hastily. Fix coming shortly... Not quite "shortly", but it's been committed as 476ce0b78713. Sorry for the wait. --nate >> >> 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/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Galaxy with postgresql
Hi Cal, Did you comment out this line? # By default, Galaxy uses a SQLite database found here #database_file = database/universe.sqlite Also, I assume you following reference: > in Galaxy configuration file, use postgresql > postgres:///galaxy_db?user=ubuntu&host=/var/run/postgresql actually looks like this in your config file: database_connection = postgres:///galaxy_db?user=ubuntu&host=/var/run/postgresql Greg Von Kuster On Apr 23, 2012, at 2:03 PM, zhengqiu cai wrote: > Hi All, > > I want to use postgresql instead of sqlite, and below is how I did the > settings: > > I am running Galaxy under the user ubuntu, so first I create the ubuntu user > sudo -u postgres createuser -D -A -P ubuntu > > Then I create the database named galaxy_db > sudo -u postgres createdb -O ubuntu galaxy_db > > in Galaxy configuration file, use postgresql > postgres:///galaxy_db?user=ubuntu&host=/var/run/postgresql > > When I start Galaxy, sqlite dialect, not postgresql is selected. I am pasting > part of the log below: > galaxy.model.migrate.check DEBUG 2012-04-23 17:59:52,676 pysqlite>=2 egg > successfully loaded for sqlite dialect > galaxy.model.migrate.check INFO 2012-04-23 17:59:52,707 At database version 93 > galaxy.tool_shed.migrate.check DEBUG 2012-04-23 17:59:52,718 pysqlite>=2 egg > successfully loaded for sqlite dialect > galaxy.tool_shed.migrate.check INFO 2012-04-23 17:59:52,730 At migrate_tools > version 1 > galaxy.model.custom_types DEBUG 2012-04-23 17:59:52,735 pysqlite>=2 egg > successfully loaded for sqlite dialect > > Is there anything wrong with my configuration? > > Thank you. > > Cai > > > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Toolshed initial upload errors
Hi Paul, The use of mercurial eggs for all tool shed mercurial related actions is now available in our central repository in change set 7102:c8f4f73e9199. This will be available in the dist repository with the next release, which I believe will be coming soon. If you're tracking the central repository, updating will hopefully solve the problems you were seeing. Thanks! Greg Von Kuster On Apr 20, 2012, at 7:39 AM, Paul-Michael Agapow wrote: > Thanks Greg, > > It's a puzzling one alright. Looking forward to testing the new version, if > only because I've run out of ideas on where to look. > > Cheers > > p > > > Paul Agapow (paul-michael.aga...@hpa.org.uk) > Bioinformatics, Health Protection Agency > > -Original Message- > From: Greg Von Kuster [mailto:g...@bx.psu.edu] > Sent: 19 April 2012 22:47 > To: Paul-Michael Agapow > Cc: 'galaxy-dev@lists.bx.psu.edu' > Subject: Re: [galaxy-dev] Toolshed initial upload errors > > Paul, > > Sorry to see you're still experiencing problems. Based on the issues you've > encountered (as well as one or two others recently) I've spent some time > re-working things to eliminate the need for installing mercurial to use a > local tool shed. We will build eggs for the mercurial package for the > various versions of Python supported by Galaxy and include them in the > distribution. > > I'm pretty close to having this finished, so it is likely that this will be > available early next week. > > I'm not sure if this will fix the problems you're seeing, but at least it > will eliminate one of the variables. > > Greg Von Kuster > > On Apr 19, 2012, at 5:02 AM, Paul-Michael Agapow wrote: > >> [For those who came in late - I've installed a local toolshed, which allows >> me to create repositories, but every time I attempt to upload files, it >> errors out with "TypeError: array item must be char". For those who come >> after me, here's what I worked out thus far.] >> >> Greg asked: >> >>> Since you've tried uploading various files with no success, the problem is >>> likely >>> to be caused by something specific to your environment - possibly the >>> version of >>> the mercurial package you're using. What version of Python are you >>> running, and >>> what version of the mercurial package do you have installed with it? Also, >>> what >>> version of Galaxy do you have, and what database / version are you using? >> >> We're CentOS, an older flavour (4), but my Mercurial is up to data (2.1.2). >> Python 2.6.4, Galaxy is 6799:40f1816d6857 (grabbed it fresh last week for >> testing), running it with sqlite. However, the Mercurial is actually >> installed local to the account I'm using, so I wonder if the toolshed is >> getting confused with another version, although hg doesn't seem to be >> installed on the system. >> >> Further investigations reveal that the files appear to be in the repo >> (database/community_files). The error manifest in the middle of Mercurial, >> in manifest.py where it attempts to coerce a Unicode string into a character >> array. (As there are some reported issues of Windows file names with Unicode >> under Mercurial, and I'm uploading from a Windows machine, I used a Mac to >> create a repo and add a file. Nope, same behaviour.) The Cistrome galaxy >> fork >> (https://bitbucket.org/cistrome/cistrome-harvard/src/e7e2fdd74496/lib/galaxy/webapps/community/controllers/upload.py) >> mentions occasional similar errors. >> >> I check the Mercurial installation: >> >> % hg --version >> Mercurial Distributed SCM (version 2.1.2+10-4d875bb546dc) >> ... >> % hg debuginstall >> Checking encoding (UTF-8)... >> Checking installed modules >> (/home/f0/paul/Installed/lib/python2.6/site-packages/mercurial)... >> Checking templates >> (/home/f0/paul/Installed/lib/python2.6/site-packages/mercurial/templates)... >> Checking commit editor... >> Checking username... >> No problems detected >> >> (Actually, I was missing a username and a user ~/.hgrc file. But making >> that, it passes. Error still persists.) >> >> Work continues. >> >> >> Paul Agapow (paul-michael.aga...@hpa.org.uk) >> Bioinformatics, Health Protection Agency >> >> - >> ** >> The information contained in the EMail and any attachments is >> confidential and intended solely and for the attention and use of >> the named addressee(s). It may not be disclosed to any other person >> without the express authority of the HPA, or the intended >> recipient, or both. If you are not the intended recipient, you must >> not disclose, copy, distribute or retain this message or any part >> of it. This footnote also confirms that this EMail has been swept >> for computer viruses, but please re-sweep any attachments before >> opening or saving. HTTP://www.HPA.org.uk >> **
[galaxy-dev] Galaxy with postgresql
Hi All, I want to use postgresql instead of sqlite, and below is how I did the settings: I am running Galaxy under the user ubuntu, so first I create the ubuntu user sudo -u postgres createuser -D -A -P ubuntu Then I create the database named galaxy_db sudo -u postgres createdb -O ubuntu galaxy_db in Galaxy configuration file, use postgresql postgres:///galaxy_db?user=ubuntu&host=/var/run/postgresql When I start Galaxy, sqlite dialect, not postgresql is selected. I am pasting part of the log below: galaxy.model.migrate.check DEBUG 2012-04-23 17:59:52,676 pysqlite>=2 egg successfully loaded for sqlite dialect galaxy.model.migrate.check INFO 2012-04-23 17:59:52,707 At database version 93 galaxy.tool_shed.migrate.check DEBUG 2012-04-23 17:59:52,718 pysqlite>=2 egg successfully loaded for sqlite dialect galaxy.tool_shed.migrate.check INFO 2012-04-23 17:59:52,730 At migrate_tools version 1 galaxy.model.custom_types DEBUG 2012-04-23 17:59:52,735 pysqlite>=2 egg successfully loaded for sqlite dialect Is there anything wrong with my configuration? Thank you. Cai ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Problem with automated install & removal with of tool with tool_data_table_conf.xml.sample
Hello Peter, This issue was fixed a while ago, but has not yet made it to the Galaxy dist repository. Since the dist repository is generally 4 to 6 weeks behind the Galaxy central repository, your local Galaxy instance will have to track the central repository instead of the dist repository in order to use any features that interact between Galaxy and the tool shed. I believe a new release to the dist repository is scheduled for some time in the next week or so, so you can wait for it if you want. Sorry for the inconvenience! Greg Von Kuster On Apr 23, 2012, at 5:53 AM, Peter Briggs wrote: > Hello > > I've encountered some problems installing and then trying to remove a tool > from the main toolshed in a local Galaxy production instance. The tool is the > tmap_wrapper but I don't think that the tool itself is the problem. > > When I tried the automated install from the toolshed, the Galaxy window came > back with "Server error" and in paster.log I found this: > > == paster.log fragment start == > galaxy.util.shed_util DEBUG 2012-04-20 15:46:15,151 Installing repository > 'tmap_wrapper' > galaxy.util.shed_util DEBUG 2012-04-20 15:46:15,186 Cloning > http://toolshed.g2.bx.psu.edu/repos/nils > homer/tmap_wrapper > galaxy.util.shed_util DEBUG 2012-04-20 15:46:17,114 Updating cloned > repository to revision "40ade4f81a30" > galaxy.tools.parameters.dynamic_options WARNING 2012-04-20 15:46:17,278 Data > table named 'tmap_indexes' is required by tool but not configured > galaxy.util.shed_util DEBUG 2012-04-20 15:46:17,322 Adding new row (or > updating an existing row) for repository 'tmap_wrapper' in the > tool_shed_repository table. > galaxy.tools.parameters.dynamic_options WARNING 2012-04-20 15:46:17,400 Data > table named 'tmap_indexes' is required by tool but not configured > 130.88.213.137 - - [20/Apr/2012:15:46:15 +0100] "POST > /galaxy/admin_toolshed/install_repository?tool_shed_url=http%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F&repo_info_dict=17a5b933699a3c40818076daffd7d763e25e8071%3A7b22746d61705f77726170706572223a205b226d617070696e6720666f7220496f6e20546f7272656e74222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6e696c73686f6d65722f746d61705f7772617070657c2022343061646534663831613330225d7d&includes_tools=True > HTTP/1.1" 500 - > "http://XX.XX.XX.XX.XX/galaxy/admin_toolshed/install_repository?tool_shed_url=http://toolshed.g2.bx.psu.edu/&repo_info_dict=17a5b933699a3c40818076daffd7d763e25e8071:7b22746d61705f77726170706572223a205b226d617070696e6720666f7220496f6e20546f7272656e74222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6e696c73686f6d65722f746d61705f7772617070657c2022343061646534663831613330225d7d&includes_tools=True"; > "Mozilla/5.0 (X11; Linux x86_64; rv:10.0.1) Gecko/20! 100101 Firefox/10.0.1" > Error - : global name > 'handle_sample_tool_data_table_conf_file' is not defined > URL: > http://XX.XX.XX.XX.XX/galaxy/admin_toolshed/install_repository?tool_shed_url=http%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F&repo_info_dict=17a5b933699a3c40818076daffd7d763e25e8071%3A7b22746d61705f77726170706572223a205b226d617070696e6720666f7220496f6e20546f7272656e74222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6e696c73686f6d65722f746d61705f7772617070657c2022343061646534663831613330225d7d&includes_tools=True > File > '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', > line 143 in __call__ > app_iter = self.application(environ, start_response) > File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', > line 80 in __call__ > return self.application(environ, start_response) > File > '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', > line 632 in __call__ > return self.application(environ, start_response) > File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 in > __call__ > body = method( trans, **kwargs ) > File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line > 173 in decorator > return func( self, trans, *args, **kwargs ) > File '/home/galaxy/galaxy-dist/lib/galaxy/web/controllers/admin_toolshed.py', > line 316 in install_repository > shed_tool_conf=shed_tool_conf ) > File '/home/galaxy/galaxy-dist/lib/galaxy/util/shed_util.py', line 890 in > load_repository_contents > repository_tools_tups = handle_missing_data_table_entry( trans.app, > tool_path, sample_files, repository_tools_tups ) > File '/home/galaxy/galaxy-dist/lib/galaxy/util/shed_util.py', line 753 in > handle_missing_data_table_entry > error, correction_msg = handle_sample_tool_data_table_conf_file( app, > sample_file ) > NameError: global name 'handle_sample_tool_data_table_conf_file' is not > defined > == paster.log fragment end == > > (I've replaced the machine name in the URLs with X's so our sysadmin won't > maim me.) It seems that the error is something to
[galaxy-dev] 回复： Error: Job output not returned from cluster
I am having the same problem when I use condor as the scheduler instead of sge. Cai --- 12年4月23日，周一, Louise-Amélie Schmitt 写道： > 发件人: Louise-Amélie Schmitt > 主题: [galaxy-dev] Error: Job output not returned from cluster > 收件人: galaxy-dev@lists.bx.psu.edu > 日期: 2012年4月23日,周一,下午5:09 > Hello everyone, > > I'm still trying to set up the job submission as the real > user, and I get a mysterious error. The job obviously runs > somewhere and when it ends it is in error state and displays > the following message: "Job output not returned from > cluster" > > In the Galaxy log I have the following lines when the job > finishes running: > > galaxy.jobs.runners.drmaa DEBUG 2012-04-23 10:36:41,509 > (1455/9161620.pbs-master2.embl.de) state change: job > finished, but failed > galaxy.jobs.runners.drmaa DEBUG 2012-04-23 10:36:41,511 Job > output not returned from cluster > galaxy.jobs DEBUG 2012-04-23 10:36:41,547 finish(): Moved > /g/funcgen/galaxy-dev/database/job_working_directory/001/1455/galaxy_dataset_2441.dat > to > /g/funcgen/galaxy-dev/database/files/002/dataset_2441.dat > galaxy.jobs DEBUG 2012-04-23 10:36:41,755 job 1455 ended > galaxy.datatypes.metadata DEBUG 2012-04-23 10:36:41,755 > Cleaning up external metadata files > galaxy.datatypes.metadata DEBUG 2012-04-23 10:36:41,768 > Failed to cleanup MetadataTempFile temp files from > /g/funcgen/galaxy-dev/database/job_working_directory/001/1455/metadata_out_HistoryDatasetAssociation_1606_npFIJM: > No JSON object could be decoded: line 1 column 0 (char 0) > > The > /g/funcgen/galaxy-dev/database/job_working_directory/001/1455/ > directory is empty and > /g/funcgen/galaxy-dev/database/files/002/dataset_2441.dat > exists but is empty. > > Any ideas about what can go wrong there? Any lead would be > immensely appreciated! > > Thanks, > L-A > > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to > this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Displaying genomic sequences in Trackster
Hi Jeremy, So, we updated our galaxy instance and now the genomic sequences can be displayed, when sufficiently zoomed in and also the visualization can be saved now. It looks really nice :-) Thanks a lot for your help. Regards, Naharajan On Apr 18, 2012, at 6:10 PM, Jeremy Goecks wrote: > Hi Naharajan, > > My best guess is that you've found some bugs. Fortunately, they are likely > fixed in galaxy-central and will soon be available in galaxy-dist (we're > planning an update in the next couple days). Once galaxy-dist is updated, > please try updating your Galaxy instance and seeing if that fixes the > problems. > > If not, let us know and we can take a closer look. > > J. > > > On Apr 18, 2012, at 9:05 AM, Naharajan Lakshmanaperumal wrote: > >> Dear all, >> >> We have our own galaxy instance and the idea is to have trackster enabled >> for users to be able to visualize NGS mapping. We were able to configure >> trackster in our instance and the visualization works fine. >> >> We have two questions regarding trackster: >> 1) We can't display genomic sequences in trackster. As per the tutorial, we >> set the location of the .2bit file in the twobit.loc file for the trackster >> to be able to display the genomic sequence but for some reason it doesn't >> display it. The name of the builds is the same in all places i.e) in >> ucsc/chrom/builds.txt and also in the .loc files. Any ideas on what else >> should be done? >> >> 2) While saving the visualization, there is always an error message saying >> "could not save visualization" and it doesn't seem to be a web browser >> issue. How do we then save the visualization? >> >> Thanks in advance, >> Naharajan >> >> >> >> >> >> >> ___ >> 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/
[galaxy-dev] Problem with automated install & removal with of tool with tool_data_table_conf.xml.sample
Hello I've encountered some problems installing and then trying to remove a tool from the main toolshed in a local Galaxy production instance. The tool is the tmap_wrapper but I don't think that the tool itself is the problem. When I tried the automated install from the toolshed, the Galaxy window came back with "Server error" and in paster.log I found this: == paster.log fragment start == galaxy.util.shed_util DEBUG 2012-04-20 15:46:15,151 Installing repository 'tmap_wrapper' galaxy.util.shed_util DEBUG 2012-04-20 15:46:15,186 Cloning http://toolshed.g2.bx.psu.edu/repos/nils homer/tmap_wrapper galaxy.util.shed_util DEBUG 2012-04-20 15:46:17,114 Updating cloned repository to revision "40ade4f81a30" galaxy.tools.parameters.dynamic_options WARNING 2012-04-20 15:46:17,278 Data table named 'tmap_indexes' is required by tool but not configured galaxy.util.shed_util DEBUG 2012-04-20 15:46:17,322 Adding new row (or updating an existing row) for repository 'tmap_wrapper' in the tool_shed_repository table. galaxy.tools.parameters.dynamic_options WARNING 2012-04-20 15:46:17,400 Data table named 'tmap_indexes' is required by tool but not configured 130.88.213.137 - - [20/Apr/2012:15:46:15 +0100] "POST /galaxy/admin_toolshed/install_repository?tool_shed_url=http%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F&repo_info_dict=17a5b933699a3c40818076daffd7d763e25e8071%3A7b22746d61705f77726170706572223a205b226d617070696e6720666f7220496f6e20546f7272656e74222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6e696c73686f6d65722f746d61705f7772617070657c2022343061646534663831613330225d7d&includes_tools=True HTTP/1.1" 500 - "http://XX.XX.XX.XX.XX/galaxy/admin_toolshed/install_repository?tool_shed_url=http://toolshed.g2.bx.psu.edu/&repo_info_dict=17a5b933699a3c40818076daffd7d763e25e8071:7b22746d61705f77726170706572223a205b226d617070696e6720666f7220496f6e20546f7272656e74222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6e696c73686f6d65722f746d61705f7772617070657c2022343061646534663831613330225d7d&includes_tools=True"; "Mozilla/5.0 (X11; Linux x86_64; rv:10.0.1) Gecko/20100101 Firefox/10.0.1" Error - : global name 'handle_sample_tool_data_table_conf_file' is not defined URL: http://XX.XX.XX.XX.XX/galaxy/admin_toolshed/install_repository?tool_shed_url=http%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F&repo_info_dict=17a5b933699a3c40818076daffd7d763e25e8071%3A7b22746d61705f77726170706572223a205b226d617070696e6720666f7220496f6e20546f7272656e74222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6e696c73686f6d65722f746d61705f7772617070657c2022343061646534663831613330225d7d&includes_tools=True File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 173 in decorator return func( self, trans, *args, **kwargs ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/controllers/admin_toolshed.py', line 316 in install_repository shed_tool_conf=shed_tool_conf ) File '/home/galaxy/galaxy-dist/lib/galaxy/util/shed_util.py', line 890 in load_repository_contents repository_tools_tups = handle_missing_data_table_entry( trans.app, tool_path, sample_files, repository_tools_tups ) File '/home/galaxy/galaxy-dist/lib/galaxy/util/shed_util.py', line 753 in handle_missing_data_table_entry error, correction_msg = handle_sample_tool_data_table_conf_file( app, sample_file ) NameError: global name 'handle_sample_tool_data_table_conf_file' is not defined == paster.log fragment end == (I've replaced the machine name in the URLs with X's so our sysadmin won't maim me.) It seems that the error is something to do with Galaxy failing to handle the tool's tool_data_table_conf.xml.sample. As far as I can tell the hg clone of the tool worked okay as the files for the tool can be found in /home/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/nilshomer/tmap_wrapper/40ade4f81a30/tmap_wrapper/tmap_wrapper_0.0.19 but the tool doesn't appear in the tool panel and isn't referenced in either the shed_tool_conf.xml or tool_conf.xml files. However: the tool does appear under the Admin -> Manage installed tool shed repositories option in Galaxy. Unfortunately attempting to uninstall it via this interface also fails with the "Server error" in the Galaxy window. This section of paster.log looks relevant here: == paster.log frag
[galaxy-dev] Error: Job output not returned from cluster
Hello everyone, I'm still trying to set up the job submission as the real user, and I get a mysterious error. The job obviously runs somewhere and when it ends it is in error state and displays the following message: "Job output not returned from cluster" In the Galaxy log I have the following lines when the job finishes running: galaxy.jobs.runners.drmaa DEBUG 2012-04-23 10:36:41,509 (1455/9161620.pbs-master2.embl.de) state change: job finished, but failed galaxy.jobs.runners.drmaa DEBUG 2012-04-23 10:36:41,511 Job output not returned from cluster galaxy.jobs DEBUG 2012-04-23 10:36:41,547 finish(): Moved /g/funcgen/galaxy-dev/database/job_working_directory/001/1455/galaxy_dataset_2441.dat to /g/funcgen/galaxy-dev/database/files/002/dataset_2441.dat galaxy.jobs DEBUG 2012-04-23 10:36:41,755 job 1455 ended galaxy.datatypes.metadata DEBUG 2012-04-23 10:36:41,755 Cleaning up external metadata files galaxy.datatypes.metadata DEBUG 2012-04-23 10:36:41,768 Failed to cleanup MetadataTempFile temp files from /g/funcgen/galaxy-dev/database/job_working_directory/001/1455/metadata_out_HistoryDatasetAssociation_1606_npFIJM: No JSON object could be decoded: line 1 column 0 (char 0) The /g/funcgen/galaxy-dev/database/job_working_directory/001/1455/ directory is empty and /g/funcgen/galaxy-dev/database/files/002/dataset_2441.dat exists but is empty. Any ideas about what can go wrong there? Any lead would be immensely appreciated! Thanks, L-A ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] dynamic_options
Hi Deepthi what do you want to use the 'dynamic_options' for? the file provided in the tag is a pyhton script, but remember the ' tag' is deprecated see: http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Ccode.3E_tag_set Regards, Hans On 04/21/2012 12:48 AM, Unknown wrote: Hi all, Is there any help available which describes about the usage of dynamic_options? Is the file should be a python executable or can we use perl? Thanks and regards, Deepthi ___ 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/
