[galaxy-dev] Password-Reset
Dear Galaxy Community, as we tried to establish the mail functionalities for our Galaxy instance, we managed to send email upon the I forgot my password user request. In the Email a Link is provided. Here two errors arise: 1. In the File galaxy/lib/galaxy/webapps/galaxy/controllers/user.pyc HTML Tags for this Email are generated, but the Email is send as plain/text, therefore the HTML Tags, as well as the (doubled) Link are visible for the user. 2. In our case, the provided link takes us to the normal user login page, where the user has no option of resetting his/her password. Can you provide me some assistance to tackle the problems? Kind Regards, Matthias Enders ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] yaml import problem on startup
So it appears the error we encountered was because we just collected the pull requests that concern the max_metada fix and applied them to the release_15.05 of galaxy cloned from mercurial. To resolve our problems we had to switch to git and then to checkout release 15.05. The below steps worked for Richard and me. (~/galaxy-dist is my production galaxy dir): cd ~ git clone https://github.com/galaxyproject/galaxy.git cd galaxy git reset --hard 3f1cec451f6dadee52a70a14fc6f6899f7aacdae cd ~/galaxy-dist hg update 17115 mv .hg .hg_backup cp -R ~/galaxy/.git . git pull #(at this point I got a merge error!) #so I did: git diff local_changes.diff cat local_changes.diff |patch -p1 -R git pull git checkout release_15.05 I do think that the metadata fixes should be pushed to mercurial quickly though. Marius On 17 July 2015 at 13:00, Marius van den Beek m.vandenb...@gmail.com wrote: Hi Richard, Reverting the patch allows normal finishing of jobs, so unfortunately it seems we get a double import somewhere in the patch ... i'm suspecting it's *from* galaxy *import* app in lib/galaxy/model/custom_types.py, but I don't know how to circumvent this. Marius On 17 July 2015 at 12:23, Marius van den Beek m.vandenb...@gmail.com wrote: Hi Richard, Well, I do have the same problem now (running bamtools), after applying the patch that should fix metadata issue we discussed yesterday. I'll dig into this. Marius On 17 July 2015 at 11:37, Poole, Richard r.po...@ucl.ac.uk wrote: Hi all, With the most recent update of Galaxy and also OS X 10.10.4 I am seeing this error message when first starting up the server: /Users/galaxy/galaxy-dist/lib/galaxy/__init__.py:63: UserWarning: Module yaml was already imported from /Library/Python/2.7/site-packages/PyYAML-3.11-py2.7-macosx-10.10-intel.egg/yaml/__init__.pyc, but /Users/galaxy/galaxy-dist/eggs/PyYAML-3.10-py2.7-macosx-10.6-intel-ucs2.egg is being added to sys.path self.check_version_conflict() This then is preventing certain tools from running correctly (such as samtools_filter (jjohnson) and they give the same error message when they fail: /Users/galaxy/galaxy-dist/lib/galaxy/__init__.py:63: UserWarning: Module yaml was already imported from /Library/Python/2.7/site-packages/PyYAML-3.11-py2.7-macosx-10.10-intel.egg/yaml/__init__.pyc, but /Users/galaxy/galaxy-dist/eggs/PyYAML-3.10-py2.7-macosx-10.6-intel-ucs2.egg is being added to sys.path self.check_version_conflict() Any thoughts? Thanks, Richard *Richard J Poole PhD* Wellcome Trust Fellow Department of Cell and Developmental Biology University College London 21 University Street, London WC1E 6DE Office (518 Rockefeller): +44 20 7679 6577 (int. 46577) Lab (529 Rockefeller): +44 20 7679 6133 (int. 46133) ___ 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: https://lists.galaxyproject.org/ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] galaxy folder tree permissions
hi everybody I'd like to ask if you think it's worthwhile is pursuing finely grained tree permissions? Would this improve security to leave out everything but only files/folders necessary for writing - to galaxy user what needs to write everything else root? Or just full perms to galaxy user on whole tree is the only way? many 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] galaxy folder tree permissions
It would be best practice to do this. Nate is working on packaging (.deb) and our Anisble setup to accomplish this - getting these permissions exactly correct I think will be a big part of that effort. All of that said - if you were really going to pursue this but just install and use the tool shed normally from the Galaxy webapp it seems kind of a wasted effort. These dependencies would be installed as the Galaxy user and run arbitrary code (from a sort of sys admin perspective). So if I were going to go through this effort I would probably try to setup a separate configuration and user for installing things from the tool shed and disable the main Galaxy instance and user from doing this. That would add considerably to this effort. Anyway - it is a best practice so I don't mean to discourage it - but realistically I don't think many Galaxy deployments have gone through this effort. -John On Mon, Jul 20, 2015 at 1:37 PM, lejeczek pelj...@yahoo.co.uk wrote: hi everybody I'd like to ask if you think it's worthwhile is pursuing finely grained tree permissions? Would this improve security to leave out everything but only files/folders necessary for writing - to galaxy user what needs to write everything else root? Or just full perms to galaxy user on whole tree is the only way? many 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: https://lists.galaxyproject.org/ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Troubleshooting
Hello, I have a problem when I try to align en FATSQ file for a ChIP-seq. I have done a FASTQ grooming because it has been performed on Illumina. No my file is a .FASTSANGER. However my file is not recognized. I see this : No fastqsanger, fastqillumina or fastqsolexa dataset collection available. How could I fix it. It seems that my fastq file as well as my fastqsanger are not recognized. Thanks a lot, Lionel ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Error sorting or uploading Bam File
Hi, Thanks for your answers. I understand that permit to load or create unsorted bam (or sorted by name) can create bug with lot of tools and it's difficult to restrict this manipulation just for few tools. But I don't understand one thing. Why can I download from the toolshed a tool which permit me to sort bam file by name (from devteam) while it's not supported by galaxy ?! Other question. Anyone can help me to write a new entry for an ‘unsorted bam’ (or namesorted) file type in the file which describe the format file uploaded ? Or do you think that I can run this sorting during the processing of the tool which require this type of sorting : so run the tool of interest and internally to the process run the sorting by name before treating the bam file. In this way do you think that Galaxy will not create an index during the process ? Thanks. Julie 2015-07-17 21:51 GMT+02:00 Frederik Coppens fr...@psb.vib-ugent.be: We also encountered this issue. As I understood it: if Galaxy gets a BAM file (either through upload or generated by a tool), it will generate metadata and indexing is part of that. This only works if the BAM file is coordinate sorted, otherwise it fails (although there is nothing wrong with the BAM file). As a lot of tools (and visualisation) require sorted BAM files, this avoids a lot of problems for users (but does create this issue). An ‘unsorted bam’ (or namesorted) file type could be a solution although this would cause the illogic situation where a ‘bam' is hierarchically not above ‘unsorted bam’ as is the case for e.g. the types of fastq. I guess changing what is now ‘bam’ to ‘sorted bam’ will cause problems for a lot of users... Frederik On 17 Jul 2015, at 21:29, Alexander Vowinkel vowinkel.alexan...@gmail.com wrote: Indeed, this would be the right approach. But so far the current strategy is quite imputed also in tools. E.g. BWA from devteam automatically sorts the bam afterwards - wanted or not. 2015-07-17 11:59 GMT-05:00 Ryan G ngsbioinformat...@gmail.com: I would think the correct approach would be to allow any bam file and if a tool requires a coordinate sorted bam and one is not provided it would make sense for the tool to fail with an error. Does galaxy itself require a coordinate sorted bam or this this so the majority of tools can function properly? Sent from my iPhone On Jul 17, 2015, at 11:08 AM, John Chilton jmchil...@gmail.com wrote: I'm not the right person to respond to this but since no one else has I will explain my limited (probably incorrect) understanding of the problem and what needs to be done. I believe Galaxy assumes all bam files are coordinated sorted by default - so Galaxy's bam datatype would be better thought of as a coordinate-sorted bam. Certain people do not want to allow non-coordinate sorted bam files because these would be allowed by Galaxy as valid as inputs to tools that expect sorted bams - and things would break. For the same reason I imagine these people would argue the bai file needs to be generated because certain tools will depend on its existence. I believe the proposed solution is to add an unsorted bam datatype to Galaxy. I don't know if there is any work in progress on this but it seems to be needed by many researchers. Hope this clarifies things somewhat, -John On Mon, Jun 29, 2015 at 11:06 AM, julie dubois dubju...@gmail.com wrote: Hi all, My galaxy is the last update and I work with samtools 1.2. I have a bug with the sorting and the upload of bam file. This bug appears only when I try to upload bam sorted by name or when I try to sort by name. When I work with bam sorted by coordinate, there is no problem. So, when I try to sort a bam file by name, this error appears under the bug icon : Tool execution generated the following error message: [bam_sort_core] merging from 20 files... *** Error in `python': double free or corruption (!prev): 0x02897990 *** Aborted (core dumped) The tool produced the following additional output: [E::hts_idx_push] chromosome blocks not continuous Galaxy attempted to build the BAM index with samtools 1.0+ but failed: [Errno 2] No such file or directory: '/data/galaxy-dist/database/job_working_directory/024/24109/__dataset_48619_metadata_temp_file_MqhjBN.bai' And the same type of error appears when I try to upload bam sorted by name. What I understand is that the bam can be sorted properly (The command line to sort is ok in a terminal with no bug and I can follow this step in the job_working_directory during the run) but Galaxy seems to fail to create a bai. For our analysis pipeline, I think the bai is not crucial, is it possible to avoid this creation of bai during uploading and sorting of bam file by name ? Is there another problem than this creation of bai ? Thanks. Julie
Re: [galaxy-dev] Troubleshooting
Hi Lionel Sounds like Galaxy does not know what format your FASTQ file is. When you click on it, what format does it show? Is it simple fastq? And how did you get it into Galaxy? You might need to manually specify the format by clicking on the Edit Attributes button (the pencil icon) and select the Datatype tab. Then set it to fastqsanger. This should allow the analysis to continue. On 20 July 2015 at 01:01, Lionel Mavoungou lionel@gmail.com wrote: Hello, I have a problem when I try to align en FATSQ file for a ChIP-seq. I have done a FASTQ grooming because it has been performed on Illumina. No my file is a .FASTSANGER. However my file is not recognized. I see this : No fastqsanger, fastqillumina or fastqsolexa dataset collection available. How could I fix it. It seems that my fastq file as well as my fastqsanger are not recognized. Thanks a lot, Lionel ___ 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: https://lists.galaxyproject.org/ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Tophat run stops
When running a Tophat job for over a hour, I get the following message and the job stops. Would anyone know why and is there a way to stop Galaxy from cleaning up the job working directory so that I can check the error log files? Dwayne galaxy.jobs.runners.local DEBUG 2015-07-14 16:54:10,478 execution finished: /data/galaxy/galaxy_prod/database/job_working_directory/000/26/galaxy_26.sh galaxy.jobs.output_checker INFO 2015-07-14 16:54:10,595 Job 26: Log: tool progress galaxy.jobs.output_checker INFO 2015-07-14 16:54:10,595 Job 26: Log: tool progress galaxy.datatypes.metadata DEBUG 2015-07-14 16:54:10,675 setting metadata externally failed for HistoryDatasetAssociation 32: [Errno 2] No such file or directory galaxy.jobs.runners.local ERROR 2015-07-14 16:54:10,754 Job wrapper finish method failed Traceback (most recent call last): File /data/galaxy/galaxy_prod/lib/galaxy/jobs/runners/local.py, line 129, in queue_job job_wrapper.finish( stdout, stderr, exit_code ) File /data/galaxy/galaxy_prod/lib/galaxy/jobs/__init__.py, line 1126, in finish dataset.datatype.set_meta( dataset, overwrite=False ) # call datatype.set_meta directly for the initial set_meta call during dataset creation File /data/galaxy/galaxy_prod/lib/galaxy/datatypes/binary.py, line 268, in set_meta proc = subprocess.Popen( args=command, stderr=open( stderr_name, 'wb' ) ) File /opt/python/2.7.9/lib/python2.7/subprocess.py, line 710, in __init__ errread, errwrite) File /opt/python/2.7.9/lib/python2.7/subprocess.py, line 1335, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
