Re: [galaxy-dev] Run a tool's workflow one by one ?
Hi John Thanks for your reply. I've copied your job_conf.xml. Unfortunately, I've got an error when I ran run.sh: galaxy.jobs DEBUG 2014-06-25 09:06:17,610 Loading job configuration from ./job_conf.xml galaxy.jobs DEBUG 2014-06-25 09:06:17,610 Read definition for handler 'main' galaxy.jobs INFO 2014-06-25 09:06:17,610 Setting handlers default to child with id 'main' Traceback (most recent call last): File my_repertory/galaxy-python/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py, line 39, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File my_repertory/galaxy-python/galaxy-dist/lib/galaxy/app.py, line 64, in __init__ self.job_config = jobs.JobConfiguration(self) File my_repertoryr/galaxy-python/galaxy-dist/lib/galaxy/jobs/__init__.py, line 107, in __init__ self.__parse_job_conf_xml(tree) File my_repertory/galaxy-python/galaxy-dist/lib/galaxy/jobs/__init__.py, line 177, in __parse_job_conf_xml self.default_destination_id = self.__get_default(destinations, self.destinations.keys()) File my_repertoryr/galaxy-python/galaxy-dist/lib/galaxy/jobs/__init__.py, line 300, in __get_default raise Exception(No %s default specified, please specify a valid id or tag with the 'default' attribute % parent.tag) Exception: No destinations default specified, please specify a valid id or tag with the 'default' attribute I don't understand where is the problem. Pat Date: Mon, 23 Jun 2014 22:19:27 -0500 Subject: Re: [galaxy-dev] Run a tool's workflow one by one ? From: jmchil...@gmail.com To: leonardsqual...@hotmail.com CC: galaxy-dev@lists.bx.psu.edu Its looks like you were going to post an error message but didn't. That might help debug problem. There is no way currently at the workflow level to force one job to wait for another before completion (other than assigning an explicit input/output relationship between the steps). There is a Trello card for this here https://trello.com/c/h5qZlgU8. I am not sure that Trello card is really the best approach for this problem though. If it really is the case that these jobs can run simultaneously and they are not implicitly dependent on each other in some way not represented in the workflow - than it is likely they are running on a machine that just doesn't have enough resources (likely memory) to run these properly. The correct solution for this I think should be properly configuring a job_conf.xml file to not let Galaxy tools over consume memory. By default Galaxy will run 4 jobs simultaneously - any job of any time - regardless of memory consumption, threads used, etc This gist (https://gist.github.com/jmchilton/ff186b01d51d401623be) contains a job_conf.xml that you can stick in your Galaxy root directory to ensure a handful of tools (I used ids hilbert, fft, slm as example ids but you should replace these values with actual values of your tool) can only run one job at a time. All other jobs will continue t concurrently run two at a time beside these. If you are using a distributed resource manager (like sun grid engine, SLURM, Condor, etc...) then the solution is a little different. You should assign these tools to job destination that consume a whole node - you would to provide more information about the cluster hardware and software configuration for me to provide an example of this. Beside that the common advice about scaling up Galaxy holds - you should configure Postgres instead of sqlite, setup a proxy (nginx or Apache), disable debug in universe_wsgi.ini, etc See https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer for details. All of these things can help in situations like this. -John On Mon, Jun 23, 2014 at 11:22 AM, Pat-74100 leonardsqual...@hotmail.com wrote: Hi ! I have a big workflow and sometime when I launched it, I got an error message for some of my tools : unable to finish job. I think it's maybe Galaxy ran multiple job so I get this error message. I'm looking to run my workflow step by step. For example this workflow: http://hcsvlab.org.au/wp-content/uploads/2014/02/PsySoundTest1.png I'm looking to run Hilbert THEN FFT THEN SLM and no Hilbert, FFT and SLM at the same time. Is it possible to make a workflow which wait to finish a job before run an another job ? Thanks ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ 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
Re: [galaxy-dev] How does Galaxy differentiate users who have not logged on?
Probably the same way by which it keeps track of you when you are logged in: setting a cookie in the browser. I didn't verify this, but that is how basically all web services do it. If you clear the galaxy cookies I expect you will end up in a new empty workspace. On 25 June 2014 01:18, Melissa Cline cl...@soe.ucsc.edu wrote: Hi folks, Quick question. When two different users use the same Galaxy instance without logging in, how does Galaxy keep their identities straight, such that when they come back to their computers the next day, they see only their own workspace and not the other user's workspace? Thanks! Melissa ___ 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 does Galaxy differentiate users who have not logged on?
Jan is correct, this is what Galaxy does. -Dannon On Wed, Jun 25, 2014 at 6:29 AM, Jan Kanis jan.c...@jankanis.nl wrote: Probably the same way by which it keeps track of you when you are logged in: setting a cookie in the browser. I didn't verify this, but that is how basically all web services do it. If you clear the galaxy cookies I expect you will end up in a new empty workspace. On 25 June 2014 01:18, Melissa Cline cl...@soe.ucsc.edu wrote: Hi folks, Quick question. When two different users use the same Galaxy instance without logging in, how does Galaxy keep their identities straight, such that when they come back to their computers the next day, they see only their own workspace and not the other user's workspace? Thanks! Melissa ___ 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/ ___ 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] Enable FTP upload in Local Galaxy instance
Dear Galaxy developers I'm trying to allow users to upload file via FTP. I've been to the tutorial website but as a beginner, I understand nothing... https://wiki.galaxyproject.org/Admin/Config/UploadviaFTP?action=showredirect=Admin%2FConfig%2FUpload+via+FTP I've configured the universe_wsgi.ini file with ftp_upload_dir = galaxy_dist/database/files/ ftp_upload_site = any adress. I use Filezilla to for FTP connecting but it doesn't works and it asks me a Port ... Can someone provide to me a simply tutorial to enable ftp upload ? Thanks Pat ___ 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_venv doesn't honour set_environment_for_install / installing lxml
Hi Janis, that is not working and it is currently not clear if we will change it. Please see the following Trello Card: https://trello.com/c/NsLJv9la/61-clean-up-tool-shed-setup-actions One of my project during the upcoming GCC hackathon is to implement a setup_python_environment, like the R, perl or ruby ones. With that in place your use case will be easy to implement. If you get your python package up and running at that time, this would be great! Cheers, Bjoern Am 24.06.2014 18:57, schrieb Jan Kanis: Ok, here is the tool_dependencies.xml. This https://gist.github.com/JanKanis/650c88001c03ac4320fe#file-not_working_tool_dependencies (also attached, if that survives the list) is what I would like my tool_dependencies.xml to look like, but it doesn't work because the installation of lxml fails, as it can't find the libxml2 headers. I am now using this https://gist.github.com/JanKanis/42b9cace27b9693a0677#file-workaround_tool_dependencies-xml as a workaround. It works because lxml is installed from a shell_command which does include the variables set from the set_environment_for_install block. This is from the blast2html tool. Jan On 24 June 2014 15:30, Dave Bouvier d...@bx.psu.edu wrote: Jan, In order to help track down this issue, could you provide the tool_dependencies.xml you're using? --Dave B. On Tue 24 Jun 2014 05:40:30 AM EDT, Jan Kanis wrote: In a tool_dependency.xml file I want to install python package lxml in a virtual environment, as a tool I'm building needs it. The python lxml package requires the libxml2 tool dependency. I have added a set_environment_for_install action that refers to the libxml2 repository, but when python/pip tries to install lxml it fails, apparently because it can't find the required headers. This appears to be because the setup_virtualenv action does not include install environment variables. It seems to me that install environment variables should be sourced for every following action that can do nontrivial things, not just shell commands. Alternatively, am I trying to install lxml the wrong way, is there a better way? (I'm running on python 2.6) 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/ ___ 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] Unable to finish job - metadata settings
Dear all, I noticed a strange behaviour in our local galaxy installation. First of all, my universe_wsgi.ini contains retry_metadata_internally = False and cleanup_job = always. The tool writes its output simply into the job_working_directory and we move it via mv static_filename.txt $output in the command-tag. This works fine. When restarting the galaxy server and executing the tool after a fresh restart, everything is ok, there are no errors. When executing the same tool a second time, galaxy brings a tool error stating that it was unable to finish the job. Nevertheless, the output files are all correct (but marked as red or failed). The error report states: Traceback (most recent call last): File /home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/local.py, line 129, in queue_job job_wrapper.finish( stdout, stderr, exit_code ) File /home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py, line 997, in finish if ( not self.external_output_metadata.external_metadata_set_successfully( dataset, self.sa_session ) and self.app.config.retry_metadata_internally ): File /home/galaxy/galaxy-dist/lib/galaxy/datatypes/metadata.py, line 731, in external_metadata_set_successfully rval, rstring = json.load( open( metadata_files.filename_results_code ) ) IOError: [Errno 2] No such file or directory: u'/home/galaxy/galaxy-dist/database/job_working_directory/000/59/metadata_results_HistoryDatasetAssociation_281_oHFjx0' And in the logfile you can find multiple entries like that: galaxy.datatypes.metadata DEBUG 2014-06-25 14:29:35,466 Failed to cleanup external metadata file (filename_results_code) for HistoryDatasetAssociation_281: [Errno 2] No such file or directory: '/home/galaxy/galaxy-dist/database/job_working_directory/000/59/metadata_results_HistoryDatasetAssociation_281_oHFjx0' The if-statement in /home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py, line 997 should evaluate to False, since self.app.config.retry_metadata_internally is set to False in the universe_wsgi.ini but it seems it doesn't in this case? Anyone having experienced such a behavior? Any suggestions how to go on and solve the issue? Many thanks! Jens ___ 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] Unable to finish job - metadata settings
Hey Jens, I have tried a few different things and I have been unable to replicate the behavior locally. Is this tool specific or configuration specific - i.e. do you see this behavior only with a specific tool or do the concatenate datasets tool experience this as well say? If it is tool specific - you (or the underlying application) may be deleting metadata_results_XXX files in the working directory as part of the job? If you are convinced the tool is not deleting these files but it is a tool-specific problem can you pass along the tool you are using (or better a minimal version of the tool that produces this behavior.) If it is configuration specific and you can get it to happen with many different tools - can you try to do it against a clean copy of galaxy-dist or galaxy-central and pass along the exact updates (universe_wsgi.ini, job_conf.xml, etc...) that you used to configure Galaxy to cause it to produce this error. Couple more things - it hasn't gone into the if in the jobs/__init__.py statement - it is doing that first check external_metadata_set_successfully when the error occurs - so I don't think it is a problem with the retry_metadata_internally configuration option. Additionally, you are using the local job runner so Galaxy will always retry_metadata_internally - the local job runner doesn't try to embed the metadata calculation into the job like the cluster job runners (so retry_metadata_internally doesn't really matter with the local job runner... right now anyway). If you don't want the metadata calculation to be embedded into the local job runner job the way cluster job runners do it (so retry_metadata_internally does in fact matter) there was an option added to the local job runner last release that I realized I hadn't documented - you can add param id=embed_metadata_in_jobTrue/param to the local job destination in job_conf.xml. More information about this new option here: https://bitbucket.org/galaxy/galaxy-central/commits/75c63b579ccdd63e0558dd9aefce7786677dbacd -John On Wed, Jun 25, 2014 at 7:41 AM, Preussner, Jens jens.preuss...@mpi-bn.mpg.de wrote: Dear all, I noticed a strange behaviour in our local galaxy installation. First of all, my universe_wsgi.ini contains “retry_metadata_internally = False” and “cleanup_job = always”. The tool writes its output simply into the job_working_directory and we move it via mv static_filename.txt $output in the command-tag. This works fine. When restarting the galaxy server and executing the tool after a fresh restart, everything is ok, there are no errors. When executing the same tool a second time, galaxy brings a “tool error” stating that it was unable to finish the job. Nevertheless, the output files are all correct (but marked as red or failed). The error report states: Traceback (most recent call last): File /home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/local.py, line 129, in queue_job job_wrapper.finish( stdout, stderr, exit_code ) File /home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py, line 997, in finish if ( not self.external_output_metadata.external_metadata_set_successfully( dataset, self.sa_session ) and self.app.config.retry_metadata_internally ): File /home/galaxy/galaxy-dist/lib/galaxy/datatypes/metadata.py, line 731, in external_metadata_set_successfully rval, rstring = json.load( open( metadata_files.filename_results_code ) ) IOError: [Errno 2] No such file or directory: u'/home/galaxy/galaxy-dist/database/job_working_directory/000/59/metadata_results_HistoryDatasetAssociation_281_oHFjx0' And in the logfile you can find multiple entries like that: galaxy.datatypes.metadata DEBUG 2014-06-25 14:29:35,466 Failed to cleanup external metadata file (filename_results_code) for HistoryDatasetAssociation_281: [Errno 2] No such file or directory: '/home/galaxy/galaxy-dist/database/job_working_directory/000/59/metadata_results_HistoryDatasetAssociation_281_oHFjx0' The if-statement in /home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py, line 997 should evaluate to False, since self.app.config.retry_metadata_internally is set to False in the universe_wsgi.ini but it seems it doesn’t in this case? Anyone having experienced such a behavior? Any suggestions how to go on and solve the issue? Many thanks! Jens ___ 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
Re: [galaxy-dev] Run a tool's workflow one by one ?
Thanks John, now it works ! You look like a Galaxy professional. Maybe you can help me again ? I've made an another topic about a FTP setting to upload large file. I've been to the Galaxy wiki tutorials but I don't understand a lot ... Pat Date: Wed, 25 Jun 2014 07:49:36 -0500 Subject: Re: [galaxy-dev] Run a tool's workflow one by one ? From: jmchil...@gmail.com To: leonardsqual...@hotmail.com CC: galaxy-dev@lists.bx.psu.edu There was a problem with the config I sent you - it defines two destinations for jobs but doesn't specify a default. I have updated the gist (and actually tried loading it in Galaxy this time): https://gist.github.com/jmchilton/ff186b01d51d401623be. Hope this helps you make progress on this issue. -John On Wed, Jun 25, 2014 at 2:09 AM, Pat-74100 leonardsqual...@hotmail.com wrote: Hi John Thanks for your reply. I've copied your job_conf.xml. Unfortunately, I've got an error when I ran run.sh: galaxy.jobs DEBUG 2014-06-25 09:06:17,610 Loading job configuration from ./job_conf.xml galaxy.jobs DEBUG 2014-06-25 09:06:17,610 Read definition for handler 'main' galaxy.jobs INFO 2014-06-25 09:06:17,610 Setting handlers default to child with id 'main' Traceback (most recent call last): File my_repertory/galaxy-python/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py, line 39, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File my_repertory/galaxy-python/galaxy-dist/lib/galaxy/app.py, line 64, in __init__ self.job_config = jobs.JobConfiguration(self) File my_repertoryr/galaxy-python/galaxy-dist/lib/galaxy/jobs/__init__.py, line 107, in __init__ self.__parse_job_conf_xml(tree) File my_repertory/galaxy-python/galaxy-dist/lib/galaxy/jobs/__init__.py, line 177, in __parse_job_conf_xml self.default_destination_id = self.__get_default(destinations, self.destinations.keys()) File my_repertoryr/galaxy-python/galaxy-dist/lib/galaxy/jobs/__init__.py, line 300, in __get_default raise Exception(No %s default specified, please specify a valid id or tag with the 'default' attribute % parent.tag) Exception: No destinations default specified, please specify a valid id or tag with the 'default' attribute I don't understand where is the problem. Pat Date: Mon, 23 Jun 2014 22:19:27 -0500 Subject: Re: [galaxy-dev] Run a tool's workflow one by one ? From: jmchil...@gmail.com To: leonardsqual...@hotmail.com CC: galaxy-dev@lists.bx.psu.edu Its looks like you were going to post an error message but didn't. That might help debug problem. There is no way currently at the workflow level to force one job to wait for another before completion (other than assigning an explicit input/output relationship between the steps). There is a Trello card for this here https://trello.com/c/h5qZlgU8. I am not sure that Trello card is really the best approach for this problem though. If it really is the case that these jobs can run simultaneously and they are not implicitly dependent on each other in some way not represented in the workflow - than it is likely they are running on a machine that just doesn't have enough resources (likely memory) to run these properly. The correct solution for this I think should be properly configuring a job_conf.xml file to not let Galaxy tools over consume memory. By default Galaxy will run 4 jobs simultaneously - any job of any time - regardless of memory consumption, threads used, etc This gist (https://gist.github.com/jmchilton/ff186b01d51d401623be) contains a job_conf.xml that you can stick in your Galaxy root directory to ensure a handful of tools (I used ids hilbert, fft, slm as example ids but you should replace these values with actual values of your tool) can only run one job at a time. All other jobs will continue t concurrently run two at a time beside these. If you are using a distributed resource manager (like sun grid engine, SLURM, Condor, etc...) then the solution is a little different. You should assign these tools to job destination that consume a whole node - you would to provide more information about the cluster hardware and software configuration for me to provide an example of this. Beside that the common advice about scaling up Galaxy holds - you should configure Postgres instead of sqlite, setup a proxy (nginx or Apache), disable debug in universe_wsgi.ini, etc See https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer for details. All of these things can help in situations like this. -John On Mon, Jun 23, 2014 at 11:22 AM, Pat-74100 leonardsqual...@hotmail.com wrote: Hi ! I have a big workflow and sometime when I launched it, I got an error message for some of my tools : unable to finish job. I think it's maybe Galaxy ran multiple job so I get this error message.
Re: [galaxy-dev] How does Galaxy differentiate users who have not logged on?
Slightly off topic, but I would like to caution that if you want to be able to ensure that your workspace is still available across time periods/browser sessions on the public site, then you should most definitely use registered accounts, as we will not be able to recover any lost anonymous histories for anyone. Thanks for using Galaxy, Dan On Jun 25, 2014, at 6:46 AM, Dannon Baker dannon.ba...@gmail.com wrote: Jan is correct, this is what Galaxy does. -Dannon On Wed, Jun 25, 2014 at 6:29 AM, Jan Kanis jan.c...@jankanis.nl wrote: Probably the same way by which it keeps track of you when you are logged in: setting a cookie in the browser. I didn't verify this, but that is how basically all web services do it. If you clear the galaxy cookies I expect you will end up in a new empty workspace. On 25 June 2014 01:18, Melissa Cline cl...@soe.ucsc.edu wrote: Hi folks, Quick question. When two different users use the same Galaxy instance without logging in, how does Galaxy keep their identities straight, such that when they come back to their computers the next day, they see only their own workspace and not the other user's workspace? Thanks! Melissa ___ 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/ ___ 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] Updated Freebayes Wrapper - Bugs
Thanks for the major update of the Freebayes wrapper, excellent! I've run into two issues, however. 1) When using set allelic scope I get the following error: Fatal error: Exit code 1 () freebayes: unrecognized option `--min-repeat-length' did you mean --min-repeat-size ? 2) When using a vcf file as input I get the following error: Fatal error: Exit code 1 () open: No such file or directory [bgzf_check_bgzf] failed to open the file: input_variant_vcf.vcf.gz [tabix++] was bgzip used to compress this file? input_variant_vcf.vcf.gz I'd be happy to help resolve these. Is there a bitbucket repo somewhere to submit pull requests? -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University ___ 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] Upload files to a data library - Invalid Paths
Hi folks, In Upload files to a data library form, seems like whatever valid path I enter for linking to data on the server, even with galaxy as user and r permissions on the folder and files - I get the invalid paths message after submitting? The basic form info: *** Invalid paths: /projects/gia/gia_analysis/blast/homologs_index_Spade_genomes/xml_reports/ Upload option: Upload files from filesystem paths File Format: blastxml Paths to upload /projects/gia/gia_analysis/blast/homologs_index_Spade_genomes/xml_reports/ Preserve directory structure? [yes or no] Copy data into Galaxy? Link to files without copying into Galaxy *** Does anyone know a trick to this? Would be nice to have more helpful error explanation here! My galaxy: 5e605ed6069f+ (stable) release_2014.02.10 . I think it is a pretty normal installation. Thanks for any tips, Regards, Damion Hsiao lab, BC Public Health Microbiology Reference Laboratory, BC Centre for Disease Control 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada ___ 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] Upload files to a data library - Invalid Paths
p.s. I do have allow_library_path_paste = True set in universe_wsgi.ini Damion ___ 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] Upload files to a data library - Invalid Paths - Solved
Solved. It was actually a file permissions thing on an ancestral folder. I will add a trello card to suggest slightly better error reporting on this though. Regards, Damion Hsiao lab, BC Public Health Microbiology Reference Laboratory, BC Centre for Disease Control 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada ___ 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] job_working_directory
I'd like to set the job_working_directory to the user's home directory. I'm using an apache proxy with ldap authentication. I'm assuming I need to strip the remote_user_maildomain off the user name to do something like... job_working_directory = ~%user/galaxy_working_directory Is this possible? ___ 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] Proposed cd-hit tool dependency change in galaxy
Hi Qi, thank you very much for you contribution. I will try to get your patch to the correct person during the upcoming Galaxy Conference. Cheers, Bjoern Am 13.06.2014 17:29, schrieb Qi, Chuyang: Hi all, When installing and testing the cd-hit tool from jjohnson from the main galaxy toolshed into my local instance of galaxy, I encountered a problem where galaxy cannot find the cd-hit program. The error was: /bin/sh: 1: cd-hit-est: not found As I debugged the problem, I found that there is an bug in the tool dependency. It installs the cd-hit programs but never moves the programs into the configurable galaxy install directory. This could cause many problems in the situation where users don't have cd-hit already installed on their computer and must depend on the tool dependency to run the tool. I propose we add the following code to the tool dependency: action type=move_file sourcecd-hit/source destination$INSTALL_DIR/destination /action action type=move_file sourcecd-hit-est/source destination$INSTALL_DIR/destination /action After I made these changes, I pushed the changes into a new repo on my local toolshed, I managed to successfully install cd-hit into a local and dev-test instance of galaxy and the cd-hit tool ran successfully. Thanks for your understanding, Charles Qi ___ 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] job_working_directory
There is certainly no flag in Galaxy to allow this. Even if you tried to hack it in - there would be some problems. Galaxy writes out some files to that working directory before running the job - so there would need to be more chown-ing and stuff happening at the beginning of the job - probably before it even got to the runner component. If Galaxy could assume these directories already existed and didn't need to run the jobs as the real user - this would be a lot easier (not easy, just easier) to hack into Galaxy - but I assume you want to run these jobs as the real user. I've created a Trello card for this request: https://trello.com/c/n1UitJTb. Sorry I don't have better news. -John On Wed, Jun 25, 2014 at 3:51 PM, Shrum, Donald C dcsh...@admin.fsu.edu wrote: I'd like to set the job_working_directory to the user's home directory. I'm using an apache proxy with ldap authentication. I'm assuming I need to strip the remote_user_maildomain off the user name to do something like... job_working_directory = ~%user/galaxy_working_directory Is this possible? ___ 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/
