[galaxy-dev] Tooshed: latest repository revision on update
Hi all; I've been working on updating the bam_to_bigwig tool in the Toolshed with an improved wrapper from Peter and Lance: http://toolshed.g2.bx.psu.edu/repository/view_repository?id=2498224736779bdb I pushed updates to the mercurial repository and now the latest revision is at 3:294e9dae5a9b. However, the pull down menu under 'Repository revision' doesn't provide the option to get the more recent revisions. The most recent version is the older 1:0ff100a057ef. Do I need to make any other changes to get the toolshed to recognize the updated revision? Apologies if I'm missing something obvious or have gotten out of sync. I'm trying to catch up on all the great toolshed improvements. Thanks much, Brad ___ 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] Tooshed: latest repository revision on update
Hi Brad, I've fixed this for you, so the new changes are now available as a revision that can be installed. The problem that caused this is a temporary known issue on the tool shed. The mercurial version (egg) is out of date and will be updated with the next Galaxy dist release. The next Galaxy release is currently scheduled for Friday. so this problem will be fixed in the tool shed at that time. Sorry for the hassle on this, Greg Von Kuster On Sep 6, 2012, at 5:59 AM, Brad Chapman wrote: Hi all; I've been working on updating the bam_to_bigwig tool in the Toolshed with an improved wrapper from Peter and Lance: http://toolshed.g2.bx.psu.edu/repository/view_repository?id=2498224736779bdb I pushed updates to the mercurial repository and now the latest revision is at 3:294e9dae5a9b. However, the pull down menu under 'Repository revision' doesn't provide the option to get the more recent revisions. The most recent version is the older 1:0ff100a057ef. Do I need to make any other changes to get the toolshed to recognize the updated revision? Apologies if I'm missing something obvious or have gotten out of sync. I'm trying to catch up on all the great toolshed improvements. Thanks much, Brad ___ 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] Tools won't go away even after deleting it from tool_conf.xml
moving to galaxy-dev this is probably related to this issue: http://dev.list.galaxyproject.org/problems-with-labels-in-the-tool-box-and-order-of-the-tools-td4655985.html Hence, try deleting integrated_tool_panel.xml first before you do a restart. Regards, Hans On 09/06/2012 01:29 PM, Makis Ladoukakis wrote: Dear Galaxy users, Has anyone experienced this problem before? In my local instance of Galaxy on a server I've deleted the path of almost all sections with their corresponding tools from tool_conf.xml (wanting to leave my own customized section) but after a restart and a new run of the run.sh there are still two of them (SNP/WGA: Data; Filters andPhenotype Association) left in the tool list with their first tool also appearing. Is there a special setting for those two? Can anyone help me? Thank you, Efthymios Ladoukakis ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev 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] Tools won't go away even after deleting it from tool_conf.xml
Dear Hans, Thank you for your help. Unfortunately after deleting the file and restarting one of them still remains. Is there anything more I could do? Regards, Efthymios Ladoukakis Date: Thu, 6 Sep 2012 14:25:11 +0200 From: h...@fmi.ch To: makis4e...@hotmail.com CC: galaxy-u...@lists.bx.psu.edu; galaxy-...@bx.psu.edu Subject: Re: Tools won't go away even after deleting it from tool_conf.xml moving to galaxy-dev this is probably related to this issue: http://dev.list.galaxyproject.org/problems-with-labels-in-the-tool-box-and-order-of-the-tools-td4655985.html Hence, try deleting integrated_tool_panel.xml first before you do a restart. Regards, Hans On 09/06/2012 01:29 PM, Makis Ladoukakis wrote: Dear Galaxy users, Has anyone experienced this problem before? In my local instance of Galaxy on a server I've deleted the path of almost all sections with their corresponding tools from tool_conf.xml (wanting to leave my own customized section) but after a restart and a new run of the run.sh there are still two of them (SNP/WGA: Data; Filters andPhenotype Association) left in the tool list with their first tool also appearing. Is there a special setting for those two? Can anyone help me? Thank you, Efthymios Ladoukakis ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev 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] Migrating a galaxy installation?
Hi Folks Our current galaxy version is pretty old (git updates are causing problems), and we are running very low on space in our filesystem which hosts /xxx/galaxy/database/files. I need to start with a clean galaxy install (possibly on a new server) on a new file system (a large Lustre volume, which is also mounted on our cluster). I do need to migrate the shared data libs, histories, workflows, etc. from the old Galaxy installation. Most of the shared data lib stuff is symlinks, which will require a change to the root path. Would it possibly be feasible to use a schema-updated copy of our current database for the new install, and do a search-and-replace procedure on the file paths in the database to deal with the new root path for the files? Anyone know which tables are involved? Any tips and advice regarding a migration of Galaxy would be really appreciated. Best regards! Fourie -- -- Prof Fourie Joubert Bioinformatics and Computational Biology Unit Department of Biochemistry University of Pretoria fourie.joub...@.up.ac.za http://www.bi.up.ac.za Tel. +27-12-420-5802 Fax. +27-12-420-5800 - This message and attachments are subject to a disclaimer. Please refer to www.it.up.ac.za/documentation/governance/disclaimer/ for full details. ___ 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] disk space warning
Hi, is there a way to warn users when the disk becomes full during a URL-based file upload (and local file upload)? I had to manually delete the temp files created during a large upload that hanged, after which Galaxy could not be re-started due to insufficient disk space. Thanks. -- Mutlu ___ 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] get wsgi headers
On 30 August 2012 14:23, Mutlu Dogruel mutludogr...@gmail.com wrote: On 29 August 2012 21:11, Nate Coraor n...@bx.psu.edu wrote: On Aug 24, 2012, at 9:48 AM, Mutlu Dogruel wrote: Hi folk, Do you know any method for reading (the extended) WSGI HTTP headers from a custom tool? If I put some debugging lines in $galaxy/lib/galaxy/web/framework/middleware/xforwardedhost.py, I can read the HTTP headers I want. But I need to access them under tools/my_script.py. Is there a way to reach the webapps http headers from there? Hi Mutlu, Do you mean the headers at the time of tool execution? Running tools (jobs) is intentionally decoupled from the state of the front end. However, you could modify the tool submission to store the header as a tool parameter and pass it in the command template. --nate Thanks. Mutlu ___ 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/ Thanks for the reply. Yes, this is what I am trying to achieve. But in my case, I need to read the headers before the tool is run, and to be more precise, just before dynamic_options creates a selection list. Because it's the dynamic_options script that needs the http header values. Essentially, I need to get some AWS keys from the http headers. We inject AWS keys and secrets into http headers on a proxy server that Galaxy is sitting behind. I have a customised upload.xml and upload.py for managing downloads from S3 buckets (I kept the original upload scripts as well). In this scenario, a list of available, permitted S3 files are generated by dynamics_options, according to the AWS keys. The user-selected file is later downloaded from Amazon using its URL. This is handled by Galaxy's native URL downloader. It works fine if I read the AWS keys from a local file, but of course, the keys do not have to be static. I just started to look into lib/galaxy/tools/parameters/dynamic_options.py, can this be a good starting point? Thanks, Best regards, -- Mutlu Hi, for those interested, this is how I solved this problem: I modified web/framework/__init__.py for setting the extra http headers we wanted. I added new objects to the app.py for holding the http headers sent by the proxy. Otherwise, it wasn't possible to retrieve them from os.environ at this depth of the code. Then I modified tools/parameters/basic.py for injecting these keys into the self.dynamic_options string variable that holds the user function's name. -- Mutlu ___ 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] How to add cuffmerge?
Hello, Our local installation of Galaxy doesn't have the 'cuffmerge' tool under NGS:RNA RNA-Seq. It has 'cufflinks', 'cuffcompare', and 'cuffdiff', but no 'cuffmerge', which is essential for the workflow. Could anyone tell me how I could add cuffmerge to the list of tools? Thank you very much. Ken. ___ 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/
