June 2014 - galaxy-dev - lists.galaxyproject.org

jobs don't get killed when histories deleted
by Jun Fan 03 Jun '14

03 Jun '14

Hi all, It seems that this problem has been reported before http://dev.list.galaxyproject.org/jobs-don-t-get-killed-when-histories-dele… and should be solved https://trello.com/card/jobs-stop-job-function-in-jobs-admin-interface-is-b…. However I am using the Apr-2014 version (at least the version with the fancy Load Data button at top of tools panel which is a quite new feature). The jobs from deleted histories still hang around in the manage jobs admin page with some cannot-finish setting_metadata jobs. The interesting thing is that the last update time is always less than 24 hours. How to delete these unwanted jobs? Best regards! Jun

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empty history pane after upgrade to latest version
by Geert Vandeweyer 03 Jun '14

03 Jun '14

Hi, Just wanted to report a small issue after upgrading galaxy to the latest revision (hg update latest_2014.06.02 ). After upgrading, the history panel did not show datasets. The main.log does not show obvious errors. this issue occurs in goolge chrome (Version 30.0.1599.114 Ubuntu 13.04 (30.0.1599.114-0ubuntu0.13.04.2). Does not occur in incognito mode, nor in firefox. Solved after cleaning out history and cache and cookies of chrome. Best, Geert -- Geert Vandeweyer, Ph.D. Department of Medical Genetics University of Antwerp Prins Boudewijnlaan 43 2650 Edegem Belgium Tel: +32 (0)3 275 97 56 E-mail: geert.vandeweyer(a)ua.ac.be http://ua.ac.be/cognitivegenetics http://www.linkedin.com/in/geertvandeweyer

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visulaization of tree produced by raxml
by Philippe Moncuquet 02 Jun '14

02 Jun '14

Hi, Do you guys have any suggestions on what tool I should use to construct tree from the output produces by raxml. There are some tree builder in Galaxy that seem not to be working with this output (correct me if I am wrong). The developer of raxml recommend dendroscope which is not available in Galaxy. Any suggestions are welcomed, Philip

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June 2, 2014 Galaxy Distribution
by Jennifer Jackson 02 Jun '14

02 Jun '14

June 2, 2014 Galaxy Distribution <http://wiki.galaxyproject.org/News/2014_06_02_Galaxy_Distribution> *News Brief <http://wiki.galaxyproject.org/DevNewsBriefs/2014_06_02>**Highlights:* * Dataset Collections introduced * Changes to database build (dbkey) organization * Enhancements to Tool configuration and Workflow options * Trackster, User Interface, and Admin panel upgrades * Significant updates to Admin and Job functionality * Tool Shed repository and API additions * Data updates plus new Security features and Bug fixes * new*: $ hg clone https://bitbucket.org/galaxy/galaxy-dist#stable *upgrade*: $ hg pull $ hg update latest_2014.06.02 getgalaxy.org <http://wiki.galaxyproject.org/Admin/Get%20Galaxy> galaxy-dist.readthedocs.org <http://galaxy-dist.readthedocs.org/> bitbucket.org/galaxy/galaxy-dist <http://bitbucket.org/galaxy/galaxy-dist>* * /Thanks for using Galaxy!/ The Galaxy Team <http://wiki.galaxyproject.org/GalaxyTeam>

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Unable to access admin after install EMBOSS 5 from galaxy test repo
by Cristian Alejandro Rojas 02 Jun '14

02 Jun '14

Hello all, I've select the emboss 5 suite to install from Galaxy test repo. After install I cant access to the admin panel. I think that is beacuse the json value is not complete (len(value):65535), and therefore the json decoder cant decode the value. In attachments I have included the debug data generated by galaxy and the file containing the "value" variable. Can anybody bring me some help? Is there some way to remove emboss without using the admin panel? Thanks in advance, best regards. *Cristian Alejandro Rojas Quintero*

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Uploading files to galaxy from a folder
by Kandalaft, Iyad 02 Jun '14

02 Jun '14

Hi Everyone I'm throwing this out there for some feedback and recommendations. Objective: Facilitate transferring large files (> 2GB) from an HPC cluster (and its associated fast tier storage) to galaxy for my clients. I enabled the FTP upload option in galaxy but it involves users learning to copy files over FTP. So, I created a galaxy folder in each users' home directory on the HPC Cluster that symbolically links to the FTP upload folder for galaxy. Hence, users can use either FTP to upload files (drag and drop in windows) or simply copy files into this folder from an ssh session on the cluster. The problem with that strategy was that galaxy had to be the owner of the file (similar to the ProFTPd configuration that sets the UID and GID of uploads files to galaxy's UID/GID). Otherwise, galaxy threw errors when it tried deleting the original file from the FTP upload folder. I could have added the galaxy user to the same group as all user but this meant that users would have to ensure the correct permissions are set on files so that galaxy can read and delete the file thereafter. The alternative involved modifying the upload.py tool to chown/chmod files that were being uploaded. Upload.py now sudo executes an external script that sets ownership to the galaxy user and corrects the permissions if required (see attachment for code modification). The galaxy user has sudo rights on this script and the script restricts chown/chmod to the ftp folder path for security reasons. I was planning to clean up the code and make it production ready by adding an option in universe_wsgi.ini for this "feature", but I thought I would check with the galaxy devs first. Am I taking the wrong approach? Is there a better alternative? As an alternative, I thought about locating the handler code for dataset.type == file and possibly making it support the SETGID sticky bits on folders. In that case, the FTP upload folder would have the sticky bit set for UID and can assume the role of the user to upload that file. Your input is much appreciated. Iyad Kandalaft Bioinformatics Application Developer Agriculture and Agri-Food Canada | Agriculture et Agroalimentaire Canada KW Neatby Bldg | éd. KW Neatby 960 Carling Ave| 960, avenue Carling Ottawa, ON | Ottawa (ON) K1A 0C6 E-mail Address / Adresse courriel: Iyad.Kandalaft(a)agr.gc.ca<mailto:Iyad.Kandalaft@agr.gc.ca> Telephone | Téléphone 613- 759-1228 Facsimile | Télécopieur 613-759-1701 Government of Canada | Gouvernement du Canada

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Re: [galaxy-dev] galaxy-dev Digest, Vol 96, Issue 1
by Kandalaft, Iyad 02 Jun '14

02 Jun '14

Hello Alejandro, You are probably using a MySQL database as a backend rather than PostgreSQL. The data definition layer in Galaxy's code uses a column type that has different maximum lengths between mysql (max chars is 2^16) and postgres (more than that). As a result, when you install a repository that has more than 2^16 character of metadata, the metadata gets truncated and you get those errors. Login in to the database backend and run the following: select id, tool_shed, name from tool_shed_repository; Find the repository in the list and write down its ID. Then run the following: Delete from tool_shed_repository where id="<PUT ID NUMBER HERE>"; Then, we need to fix the table column type for your database. Note that my database table has been fixed with the new datatype "mediumblob". | metadata | mediumblob | YES | | NULL | | You should do a backup of the database before you proceed. Run the following command to modify the metadata column on table tool_shed_repository to the mediumblob data type to allow a large amount of metadata. ALTER TABLE tool_shed_repository MODIFY metadata MEDIUMBLOB NULL; I had opened a Trello card about this but haven't had time to push a fix. Regards, Iyad Kandalaft Bioinformatics Application Developer Agriculture and Agri-Food Canada | Agriculture et Agroalimentaire Canada KW Neatby Bldg | éd. KW Neatby 960 Carling Ave| 960, avenue Carling Ottawa, ON | Ottawa (ON) K1A 0C6 E-mail Address / Adresse courriel: Iyad.Kandalaft(a)agr.gc.ca Telephone | Téléphone 613- 759-1228 Facsimile | Télécopieur 613-759-1701 Government of Canada | Gouvernement du Canada -----Original Message----- From: galaxy-dev-bounces(a)lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of galaxy-dev-request(a)lists.bx.psu.edu Sent: Monday, June 02, 2014 12:00 PM To: galaxy-dev(a)lists.bx.psu.edu Subject: galaxy-dev Digest, Vol 96, Issue 1 Send galaxy-dev mailing list submissions to galaxy-dev(a)lists.bx.psu.edu To subscribe or unsubscribe via the World Wide Web, visit http://lists.bx.psu.edu/listinfo/galaxy-dev or, via email, send a message with subject or body 'help' to galaxy-dev-request(a)lists.bx.psu.edu You can reach the person managing the list at galaxy-dev-owner(a)lists.bx.psu.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of galaxy-dev digest..." HEY! This is important! If you reply to a thread in a digest, please 1. Change the subject of your response from "Galaxy-dev Digest Vol ..." to the original subject for the thread. 2. Strip out everything else in the digest that is not part of the thread you are responding to. Why? 1. This will keep the subject meaningful. People will have some idea from the subject line if they should read it or not. 2. Not doing this greatly increases the number of emails that match search queries, but that aren't actually informative. Today's Topics: 1. Unable to access admin after install EMBOSS 5 from galaxy test repo (Cristian Alejandro Rojas) 2. Re: Uploading files to galaxy from a folder (John Chilton) 3. Re: Uploading files to galaxy from a folder (Kandalaft, Iyad) 4. Installing galaxy with Apache (Matthias Enders) 5. Re: Cluster Admins - Call for experiences/issues encountered (Bj?rn Gr?ning) 6. Re: stdout in history (Daniel Blankenberg) 7. Re: Cluster Admins - Call for experiences/issues encountered (Eric Rasche) 8. Re: Cluster Admins - Call for experiences/issues encountered (Bj?rn Gr?ning) 9. Re: New tool on TestToolShed still not tested (Dave Bouvier) ---------------------------------------------------------------------- Message: 1 Date: Sun, 1 Jun 2014 13:32:15 -0500 From: Cristian Alejandro Rojas <alejandro.0317(a)gmail.com> To: galaxy-dev(a)lists.bx.psu.edu Subject: [galaxy-dev] Unable to access admin after install EMBOSS 5 from galaxy test repo Message-ID: <CALk039YufzUvf_iQ1CQuq9Sh3J9t94kMakOD6u87=qRGU0mPig(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hello all, I've select the emboss 5 suite to install from Galaxy test repo. After install I cant access to the admin panel. I think that is beacuse the json value is not complete (len(value):65535), and therefore the json decoder cant decode the value. In attachments I have included the debug data generated by galaxy and the file containing the "value" variable. Can anybody bring me some help? Is there some way to remove emboss without using the admin panel? Thanks in advance, best regards. *Cristian Alejandro Rojas Quintero*

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New tool on TestToolShed still not tested
by Peter Cock 02 Jun '14

02 Jun '14

Hi guys, I updated this new tool on Wednesday last week, but it still has no functional test results: http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast_rbh Has it been excluded for some reason? If so, could some indicator be shown (at least to the tool authors)? I looked over some of my other tools and the test dates are quite variable. I thought you had gone from nightly tests to every second night - but is the scheme now more complex, or have there been technical difficulties? Thanks, Peter

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Cluster Admins - Call for experiences/issues encountered
by Eric Rasche 02 Jun '14

02 Jun '14

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 This is specifically to galaxy administrators and developers who have worked with galaxy and cluster deployment. If you have successfully deployed a galaxy instance backed by one (or more) clusters, I'm looking to hear about your experience; - - the configuration - - any pitfalls encountered - - any extra tools that needed to be installed - - any ugly hacks you had to implement The current cluster documentation is somewhat lacking, and I'm willing to compile everyone's experiences deploying to clusters if you're willing to send them in. I'll update the cluster page on the wiki as I receive replies and can allocate time. By way of example, here's the summary of what I would reply to this email with my experiences deploying to an HTCondor cluster - - HTcondor ran fine, accepted jobs and worked for all users - - Connecting galaxy to it would result in some jobs running/some jobs failing. It was determined that those jobs which ran, were only on localhost. - - This was a result of the fact that galaxy's home directory/data was not exported - - Galaxy was made an LDAP user and a folder created in the correct location on all computers - - This still failed, as galaxy does not transfer files by default (as far as I can tell), even though that's available in HTCondor - - Finally galaxy's home directory was NFS exported and things seemed to work. Cheers, Eric - -- Eric Rasche Programmer II Center for Phage Technology Texas A&M University College Station, TX 77843 404-692-2048 esr(a)tamu.edu rasche.eric(a)yandex.ru -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) iQIcBAEBAgAGBQJThL4PAAoJEMqDXdrsMcpVJ0wP/jPFrTxRYnWcavbUxhht8tWE VDhid2pst7o+qkkLAUylPyNzJz31movsU1Gd2FJLP4+RHb3lhy2GWm8mR9G4JuMM g7fHAwIRj1qTT5tMXAEN6EoCtrValZH0EkIQPaFUPIiN1wzGTTDP56V+L6f3xQNg zglk2GTO+hM+AunYGuDugDvdKTPyKgR1K2vaCNdc2kZlvQZe7TlOHZEbXaoDGTY4 vwHcNR0+8fvf6Hs1liCuCuh8nlTBABZLxMl5LgxOaZqbaAVQWsqXNdh1tF/rlERL +PlNv5HRBWz26iGE04jbAD1pKmxg33Knl3l4MXrUnB5ZJ2dIDJL0YHOhXM3mjI4T Hf8mv/iVr21xx3zrrAbAlRIt3Npw4DtaGSqBFdKvnxQZygjKEF7ZKTGfA4xLNRHh 4dPElUpv8b3jUe2GqhXyrmHYuBdWqBC5Y/ii0k4c/bHjoXW6yg0mPs7po7i5+5JS wnO3mfoFhnyEALd45EBprkQY+kx05zjSg4ntpeywl8fIM2uGT0GyANA0/prKhcmB 5PiYUejsaDTY4GigiiZqz0tnC5z7VDyjByfyl7ufNaaCWNRXlTNIzH0ePy0ZjLrU Sj8XyI1XoOSdtyxxvNNe8OPDxxffnJxi0rres4Q3CC/EbZK4vBF7chsisHd28Q29 M1e+lNdO8FBIoy5+MR3H =6Jbk -----END PGP SIGNATURE-----

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stdout in history
by Neil.Burdett＠csiro.au 02 Jun '14

02 Jun '14

Hi, It seems that the first 4/5 lines that are printed in the source code tools appear in the history (when expended) and in stdout link. Is there anyway to stop "print" statements appearing in the history panel? Thanks Neil

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