Re: [galaxy-dev] Failure when preparing job on blastp
Hi Peter v H, Which version of Galaxy are you running? Which version of ncbi_blast_tools are you running? (ideally down to the ToolShed revision) My guess is that since this used to be .extra_files_path perhaps your Galaxy is too old for .files_path to work? https://github.com/peterjc/galaxy_blast/commit/2bbbf7f361ada20bf1b5bd777fae6e0cb52c4a38 Thanks, Peter C. On Tue, Jul 21, 2015 at 3:08 PM, Peter van Heusden p...@sanbi.ac.za wrote: Hi there I'm trying to use the blastp tools from the ncbi_blast_tools, but every time I try and run a job I get the following error: Traceback (most recent call last): File /net/datasrv3hs.sanbi.ac.za/cip0/software/galaxy/galaxysrv/galaxy/lib/galaxy/jobs/runners/__init__.py, line 163, in prepare_job job_wrapper.prepare() File /net/datasrv3hs.sanbi.ac.za/cip0/software/galaxy/galaxysrv/galaxy/lib/galaxy/jobs/__init__.py, line 859, in prepare self.command_line, self.extra_filenames, self.environment_variables = tool_evaluator.build() File /net/datasrv3hs.sanbi.ac.za/cip0/software/galaxy/galaxysrv/galaxy/lib/galaxy/tools/evaluation.py, line 422, in build raise e NotFound: cannot find 'files_path' while searching for 'db_opts.histdb.files_path' This is happening when expanding the tool template. The BLAST db in in the history (thus the reference to histdb) but why can it not find this attribute? 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: 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/
Re: [galaxy-dev] Connection reset by peer
Yeah - that workflow run endpoint is fairly problematic since it requires to workflow to be completely scheduled. There is code in Galaxy and an API endpoint that will schedule the workflow in the background - but bioblend hasn't been updated to use this yet. I've created a bioblend issue to track progress on this - https://github.com/galaxyproject/bioblend/issues/153. There are various examples inside the test code of who to use this API endpoint - basically I think you will want to POST to /api/workflows/workflow_id/invocations instead of /api/workflows. Hopefully I can find some time to update bioblend soon to do this. -John On Tue, Jul 21, 2015 at 4:01 PM, COUNTOURIS Hector hector.countou...@aphp.fr wrote: Hello, i'm actually having a message of connection reset by peer when i'm launching a long API request (upload files only links actually, run the workflow other them and retrieve the results into a specific folder). The workflow is working fine when i proceed to an analysis file by file but when it comes to several file processing (like 10 or more), this exception appear. I'm working with Bioblend on a local instance with a postgres SGBD. I've perfom the database performance enhancement you suggest for production mode. But right know i don't have any Apache or Nginx server. Is that mandatory ? Thanks in advance for your help. Best regards. HC. ___ 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/
Re: [galaxy-dev] Troubleshooting
Hello Peter, Thanks a lot. It worked well. However the run stopped after a few minutes. Here is the message : Error aligning sequence. Error reading ebwt array: returned 113175904, length was 823263360 Your index files may be corrupt; please try re-building or re-downloading. A complete index consists of 6 files: XYZ.1.ebwt, XYZ.2.ebwt, XYZ.3.ebwt, XYZ.4.ebwt, X Honestly I have no idea what it means. I tried to upload the fastq file from a big Cell paper to have an example of analysis. Do you think that the original Fastq from the paper could have a problem (as an example : an home made way to process samples ?) Thanks again, Lionel 2015-07-20 14:57 GMT-04:00 Peter van Heusden p...@sanbi.ac.za: 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/
Re: [galaxy-dev] galaxy folder tree permissions
Apologies John - hit reply instead of reply-all first time around... Maybe this is the right place to ask about the shed_tools and tool deps directory permissions. Installing tools from the web I get a mixed bag of folder permission, some at 775, some at 777 drwxrwxr-x 43 galaxy galaxy 4.0K Apr 9 16:44 devteam drwxrwxr-x 27 galaxy galaxy 4.0K Jul 10 14:15 iuc drwxrwxr-x 4 galaxy galaxy 60 Mar 27 11:24 lparsons drwxrwxrwx 3 galaxy galaxy 28 Jun 19 09:42 ngsplot drwxrwxrwx 3 galaxy galaxy 32 Apr 9 16:40 pjbriggs drwxrwxrwx 3 galaxy galaxy 24 Jun 23 16:41 readline drwxrwxrwx 3 galaxy galaxy 27 Jul 10 14:10 rnastar drwxrwxr-x 6 galaxy galaxy 72 Jun 23 16:40 samtools drwxrwxrwx 3 galaxy galaxy 26 Jun 23 16:36 sqlite On a 'run as real user' setup all users need read/execute access so you can't lock down the upper-level directory holding the tools and deps. Having write open to anyone when a tool is installed is then pretty nasty as in theory someone could maliciously modify something. Wondering if I'm missing some setting in Galaxy somewhere that would result in 775 all the time for newly installed tools and their deps? -- David Trudgian Ph.D. Computational Scientist, BioHPC UT Southwestern Medical Center Dallas, TX 75390-9039 Tel: (214) 648-4833 Please contact biohpc-help@utsouthwestern with general BioHPC inquries. -Original Message- From: galaxy-dev [mailto:galaxy-dev-boun...@lists.galaxyproject.org] On Behalf Of John Chilton Sent: Monday, July 20, 2015 7:59 AM To: lejeczek Cc: galaxy-dev@lists.galaxyproject.org Subject: 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/ UT Southwestern Medical Center The future of medicine, today. ___ 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] Failure when preparing job on blastp
Thanks Peter, Yes, you are using the latest release published to the Tool Shed, aka v0.1.03 (internal changes): https://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus/c16c30e9ad5b I've filed this as an issue on the GitHub repository, https://github.com/peterjc/galaxy_blast/issues/69 If you are also on GitHub we can discuss this there, where I've CC'd John and Bjoern for their thoughts. Something simple you could try now is going back to an older ncbi_blast_plus via the Tool Shed? The previous release 2fe07f50a41e aka v0.1.01 used the alternative form $db_opts.histdb.extra_files_path rather than the current $db_opts.histdb.files_path which appears to be failing. Thanks, Peter On Tue, Jul 21, 2015 at 6:17 PM, Peter van Heusden p...@sanbi.ac.za wrote: This is release_15.07 (last commit listed is 39f6730e5f50b54f372b8c1e17d86d8936b5899f) and ncbi_blast_plus c16c30e9ad5b. So no, its not an old Galaxy. On 21 July 2015 at 17:37, Peter Cock p.j.a.c...@googlemail.com wrote: Hi Peter v H, Which version of Galaxy are you running? Which version of ncbi_blast_tools are you running? (ideally down to the ToolShed revision) My guess is that since this used to be .extra_files_path perhaps your Galaxy is too old for .files_path to work? https://github.com/peterjc/galaxy_blast/commit/2bbbf7f361ada20bf1b5bd777fae6e0cb52c4a38 Thanks, Peter C. On Tue, Jul 21, 2015 at 3:08 PM, Peter van Heusden p...@sanbi.ac.za wrote: Hi there I'm trying to use the blastp tools from the ncbi_blast_tools, but every time I try and run a job I get the following error: Traceback (most recent call last): File /net/datasrv3hs.sanbi.ac.za/cip0/software/galaxy/galaxysrv/galaxy/lib/galaxy/jobs/runners/__init__.py, line 163, in prepare_job job_wrapper.prepare() File /net/datasrv3hs.sanbi.ac.za/cip0/software/galaxy/galaxysrv/galaxy/lib/galaxy/jobs/__init__.py, line 859, in prepare self.command_line, self.extra_filenames, self.environment_variables = tool_evaluator.build() File /net/datasrv3hs.sanbi.ac.za/cip0/software/galaxy/galaxysrv/galaxy/lib/galaxy/tools/evaluation.py, line 422, in build raise e NotFound: cannot find 'files_path' while searching for 'db_opts.histdb.files_path' This is happening when expanding the tool template. The BLAST db in in the history (thus the reference to histdb) but why can it not find this attribute? 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: 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/ ___ 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] Failure when preparing job on blastp
Previous revision of ncbi_blast_plus works like a charm, thanks. On 21 July 2015 at 19:57, Peter Cock p.j.a.c...@googlemail.com wrote: Thanks Peter, Yes, you are using the latest release published to the Tool Shed, aka v0.1.03 (internal changes): https://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus/c16c30e9ad5b I've filed this as an issue on the GitHub repository, https://github.com/peterjc/galaxy_blast/issues/69 If you are also on GitHub we can discuss this there, where I've CC'd John and Bjoern for their thoughts. Something simple you could try now is going back to an older ncbi_blast_plus via the Tool Shed? The previous release 2fe07f50a41e aka v0.1.01 used the alternative form $db_opts.histdb.extra_files_path rather than the current $db_opts.histdb.files_path which appears to be failing. Thanks, Peter On Tue, Jul 21, 2015 at 6:17 PM, Peter van Heusden p...@sanbi.ac.za wrote: This is release_15.07 (last commit listed is 39f6730e5f50b54f372b8c1e17d86d8936b5899f) and ncbi_blast_plus c16c30e9ad5b. So no, its not an old Galaxy. On 21 July 2015 at 17:37, Peter Cock p.j.a.c...@googlemail.com wrote: Hi Peter v H, Which version of Galaxy are you running? Which version of ncbi_blast_tools are you running? (ideally down to the ToolShed revision) My guess is that since this used to be .extra_files_path perhaps your Galaxy is too old for .files_path to work? https://github.com/peterjc/galaxy_blast/commit/2bbbf7f361ada20bf1b5bd777fae6e0cb52c4a38 Thanks, Peter C. On Tue, Jul 21, 2015 at 3:08 PM, Peter van Heusden p...@sanbi.ac.za wrote: Hi there I'm trying to use the blastp tools from the ncbi_blast_tools, but every time I try and run a job I get the following error: Traceback (most recent call last): File /net/ datasrv3hs.sanbi.ac.za/cip0/software/galaxy/galaxysrv/galaxy/lib/galaxy/jobs/runners/__init__.py , line 163, in prepare_job job_wrapper.prepare() File /net/ datasrv3hs.sanbi.ac.za/cip0/software/galaxy/galaxysrv/galaxy/lib/galaxy/jobs/__init__.py , line 859, in prepare self.command_line, self.extra_filenames, self.environment_variables = tool_evaluator.build() File /net/ datasrv3hs.sanbi.ac.za/cip0/software/galaxy/galaxysrv/galaxy/lib/galaxy/tools/evaluation.py , line 422, in build raise e NotFound: cannot find 'files_path' while searching for 'db_opts.histdb.files_path' This is happening when expanding the tool template. The BLAST db in in the history (thus the reference to histdb) but why can it not find this attribute? 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: 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/ ___ 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] Failure when preparing job on blastp
Thanks Peter for your very quick reply confirming that workaround. I'll wait to hear from John, as the real fix may be on the Galaxy side, but we may need to push an update to the Tool Shed to use the older .extra_files_path form in the short term. Thanks, Peter On Tue, Jul 21, 2015 at 7:22 PM, Peter van Heusden p...@sanbi.ac.za wrote: Previous revision of ncbi_blast_plus works like a charm, thanks. On 21 July 2015 at 19:57, Peter Cock p.j.a.c...@googlemail.com wrote: Thanks Peter, Yes, you are using the latest release published to the Tool Shed, aka v0.1.03 (internal changes): https://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus/c16c30e9ad5b I've filed this as an issue on the GitHub repository, https://github.com/peterjc/galaxy_blast/issues/69 If you are also on GitHub we can discuss this there, where I've CC'd John and Bjoern for their thoughts. Something simple you could try now is going back to an older ncbi_blast_plus via the Tool Shed? The previous release 2fe07f50a41e aka v0.1.01 used the alternative form $db_opts.histdb.extra_files_path rather than the current $db_opts.histdb.files_path which appears to be failing. Thanks, Peter On Tue, Jul 21, 2015 at 6:17 PM, Peter van Heusden p...@sanbi.ac.za wrote: This is release_15.07 (last commit listed is 39f6730e5f50b54f372b8c1e17d86d8936b5899f) and ncbi_blast_plus c16c30e9ad5b. So no, its not an old Galaxy. On 21 July 2015 at 17:37, Peter Cock p.j.a.c...@googlemail.com wrote: Hi Peter v H, Which version of Galaxy are you running? Which version of ncbi_blast_tools are you running? (ideally down to the ToolShed revision) My guess is that since this used to be .extra_files_path perhaps your Galaxy is too old for .files_path to work? https://github.com/peterjc/galaxy_blast/commit/2bbbf7f361ada20bf1b5bd777fae6e0cb52c4a38 Thanks, Peter C. On Tue, Jul 21, 2015 at 3:08 PM, Peter van Heusden p...@sanbi.ac.za wrote: Hi there I'm trying to use the blastp tools from the ncbi_blast_tools, but every time I try and run a job I get the following error: Traceback (most recent call last): File /net/datasrv3hs.sanbi.ac.za/cip0/software/galaxy/galaxysrv/galaxy/lib/galaxy/jobs/runners/__init__.py, line 163, in prepare_job job_wrapper.prepare() File /net/datasrv3hs.sanbi.ac.za/cip0/software/galaxy/galaxysrv/galaxy/lib/galaxy/jobs/__init__.py, line 859, in prepare self.command_line, self.extra_filenames, self.environment_variables = tool_evaluator.build() File /net/datasrv3hs.sanbi.ac.za/cip0/software/galaxy/galaxysrv/galaxy/lib/galaxy/tools/evaluation.py, line 422, in build raise e NotFound: cannot find 'files_path' while searching for 'db_opts.histdb.files_path' This is happening when expanding the tool template. The BLAST db in in the history (thus the reference to histdb) but why can it not find this attribute? 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: 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/ ___ 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/
Re: [galaxy-dev] Object-Store, setting filetypes crashes Galaxy
Hello all, This is resurrecting an old thread, but using $input.extra_files_path rather than $input.files_path explained an unfortunate regression in the BLAST+ wrappers reported earlier today: https://github.com/peterjc/galaxy_blast/issues/69 Thanks John for his detective work. Given $output.files_path is considered preferable over $output.extra_files_path it would be great to have the same alias available for input parameters for consistency (although as per John's old email below, this may be tricky). Regards, Peter On Fri, Jun 20, 2014 at 5:15 AM, John Chilton jmchil...@gmail.com wrote: Bjoern, The following patch should put out the fire... https://bitbucket.org/galaxy/galaxy-central/commits/d781366bc120787e201b73a4dd99b56282169d86 TL;DR - After this patch $output.extra_files_path is the same thing as $output.files_path - which is to say not broken in a bunch of corner cases and slightly less efficient in the most vanilla Galaxy deployments. $input.extra_files_path however is a bit tricky if the path doesn't exist (probably not the case with your deployment Bjoern) - for disk object stores it just returns the non-existent path - for the nested object store it throws an error and the tool won't run. I had a patch to synchronize the behavior (https://gist.github.com/jmchilton/d05bcf02874762cdb829) - but I cannot say for sure the current behavior isn't intentional (Dannon, Nate - want to weigh in on this?). -John ___ 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] Change from Bitbucket to git
Thanks Marius, it does not look like it's working for me. There are to many changes in git diff... the git pull and cat local_changes.diff |patch -p1 -R gives me an endless list of differences. Cheers Jochen On 21.07.2015 11:41, Marius van den Beek wrote: Hi Jochen, I recently did this. Instructions are here: https://wiki.galaxyproject.org/Develop/SourceCode This has worked for 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 Best, Marius On 21 July 2015 at 11:36, Jochen Bick jochen.b...@usys.ethz.ch wrote: Hi, is it possible to change from bitbucket to git? So I would like future-update my galaxy from git instead from bitbucket. Cheers Jochen ___ 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] Change from Bitbucket to git
Hi Jochen, I recently took a probably more labour intensive approach. # backup! # mv prev-installation to somewhere else # git clone to old-location # git checkout -b master origin/master # and copy over every config, tool xml, tool dependency directory, tool-data loc files from the prev-installation to the new git one # add your own code changes if you have any that you want to keep # ./run.sh or manage_db.sh upgrade # check log and probably copy some more missing files The upside for me was that I could finally remove all the junk that our installation has been collecting for the last couple of year. Cheers, Jelle On Tue, Jul 21, 2015 at 12:45 PM, Jochen Bick jochen.b...@usys.ethz.ch wrote: Thanks Marius, it does not look like it's working for me. There are to many changes in git diff... the git pull and cat local_changes.diff |patch -p1 -R gives me an endless list of differences. Cheers Jochen On 21.07.2015 11:41, Marius van den Beek wrote: Hi Jochen, I recently did this. Instructions are here: https://wiki.galaxyproject.org/Develop/SourceCode This has worked for 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 Best, Marius On 21 July 2015 at 11:36, Jochen Bick jochen.b...@usys.ethz.ch wrote: Hi, is it possible to change from bitbucket to git? So I would like future-update my galaxy from git instead from bitbucket. Cheers Jochen ___ 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] Change from Bitbucket to git
Hi, is it possible to change from bitbucket to git? So I would like future-update my galaxy from git instead from bitbucket. Cheers Jochen ___ 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] Change from Bitbucket to git
Hi Jochen, I recently did this. Instructions are here: https://wiki.galaxyproject.org/Develop/SourceCode This has worked for 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 Best, Marius On 21 July 2015 at 11:36, Jochen Bick jochen.b...@usys.ethz.ch wrote: Hi, is it possible to change from bitbucket to git? So I would like future-update my galaxy from git instead from bitbucket. Cheers Jochen ___ 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] Failure when preparing job on blastp
Hi there I'm trying to use the blastp tools from the ncbi_blast_tools, but every time I try and run a job I get the following error: Traceback (most recent call last): File /net/ datasrv3hs.sanbi.ac.za/cip0/software/galaxy/galaxysrv/galaxy/lib/galaxy/jobs/runners/__init__.py, line 163, in prepare_job job_wrapper.prepare() File /net/ datasrv3hs.sanbi.ac.za/cip0/software/galaxy/galaxysrv/galaxy/lib/galaxy/jobs/__init__.py, line 859, in prepare self.command_line, self.extra_filenames, self.environment_variables = tool_evaluator.build() File /net/ datasrv3hs.sanbi.ac.za/cip0/software/galaxy/galaxysrv/galaxy/lib/galaxy/tools/evaluation.py, line 422, in build raise e NotFound: cannot find 'files_path' while searching for 'db_opts.histdb.files_path' This is happening when expanding the tool template. The BLAST db in in the history (thus the reference to histdb) but why can it not find this attribute? 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
