- galaxy-dev - lists.galaxyproject.org

sysadmin help
by Shrum, Donald C 29 Jan '14

29 Jan '14

Hi all, I could use a little basic help. I'm setting up a proof of concept galaxy server that will run in conjunction with our HPC here at FSU. Ultimately this will serve as a template where we will allow some users to run galaxy on a VM and use it as a mechanism for submitting/managing jobs on our cluster. I've installed Galaxy on a VM that mounts our HPC file system and managed to import an ecoli .fa file. My plan was to run bowtie2 on our HPC. https://rcc.fsu.edu/software/bowtie2 Disclaimer... I'm a sysadmin and other than compiling software my knowledge in bioinformatics is sorely lacking ;) I'm looking at the docs here https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#PBS I get a 404 for details on Torque - http://www.clusterresources.com/pages/products/torque-resource-manager.php Any help would be greatly appreciated. Additionally, if my intended use for Galaxy seems out of the scope of what would be useful, please let me know. Thanks, Donny Shrum FSU Research Computing Center

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Problem with editing permissions on Galaxy libraries
by Christophe Antoniewski 29 Jan '14

29 Jan '14

Hi, Since an undetermined period of time in our instance, the "edit permission" panel under admin management of libraries shows an unexpected aspect: The "modify library item" part of the form is normal, with 2 fields for Roles associated and Roles not associated. However, none of the other parts of the form (access library, add library item, manage library permissions) have the "Roles not associated" fields. I am not saying that these fields are empty, they are just absent. With the consequence that we cannot really manage anymore the library access rights. Any hints ? Is it a bug or a feature (such as a consequence of managing bad something else somewhere else) ? Thanks Chris Christophe Antoniewski Drosophila Genetics and Epigenetics Laboratoire de Biologie du Développement 9, Quai St Bernard, Boîte courrier 24 75252 Paris Cedex 05 http://bio-dev.snv.jussieu.fr/ Tel +33 1 44 27 34 39 Fax +33 1 44 27 34 45 Mobile +33 6 68 60 51 50 http://drosophile.org

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Re: [galaxy-dev] datatype for executables
by Ketan Maheshwari 29 Jan '14

29 Jan '14

Hi Peter, Thanks for the advice. I was trying to say that the potential users for this case will run the tool on: 1. cloud instances that they own 2. PBS/Torque/SLURM interfaced HPC resources which they will have authenticated access to. This means that say in the worse case if some one chooses to run a forkbomb, it will only kill her own resource. In my opinion this is no less secure than say I wrap a forkbomb into a torque script and submit it to my department cluster. I am accountable and traceable to any harm I do this way. The benefit to users on the other hand will be that they can easily test their arbitrary applications to run on a larger scale via the task-parallelism provided by Swift. Once a user is satisfied with the behavior of her task on a compute node via Galaxy, she can follow our recipe which will concretize her implementation as a tool to be used in practice. Were there any scenarios you had in mind that would lead to security issues? Thanks, Ketan On Tue, Jan 28, 2014 at 4:17 PM, Peter Cock <p.j.a.cock(a)googlemail.com>wrote: > On Tue, Jan 28, 2014 at 8:26 PM, Ketan Maheshwari <ketan(a)mcs.anl.gov> > wrote: > > > > Is it possible to write a type file "bin_or_exe" which can detect the > > executable bit of data before they are part of Galaxy's indexed data. > > > > Thanks, > > Ketan > > You haven't convinced me this is a good idea, but I would try this > by defining a new datatype class in Python with a sniffer method > which just checks for the executable bit (probably defined as a > subclass of the binary datatype, see [1]) and then add this and > its sniffer to the datatype XML file. > > Peter > > [1] > https://bitbucket.org/galaxy/galaxy-central/src/default/lib/galaxy/datatype… > -- Ketan

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404
by Shrum, Donald C 29 Jan '14

29 Jan '14

And I just realized that 404 is on a non galaxy site..... Sorry about that ;)

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datatype for executables
by Ketan Maheshwari 28 Jan '14

28 Jan '14

Is there a data type in Galaxy that identifies executables uniquely, eg. from the executable bit in the file perms or some other way? Thanks, -- Ketan

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Re: [galaxy-dev] ProFFTPd-1.3.4d no longer able to authenticate users from Postgresql database
by Dooley, Damion 28 Jan '14

28 Jan '14

After following some of the links that this thread referenced (since it is totally related to the one I put in on friday), I found the "rollback" solution, to disable pbkdf2 authentication. I did attempt pbkdf2 for a while, but openssl upgrade and pbkdf2 recompile issues have led me to drop that. Can someone PLEASE document the pbkdf2 issues and this disable feature on the galaxy wiki page: https://wiki.galaxyproject.org/Admin/Config/Upload%20via%20FTP Message: 2 Date: Mon, 27 Jan 2014 17:08:24 +0000 From: "Hazard, E. Starr" <hazards(a)musc.edu> Subject: Re: [galaxy-dev] ProFFTPd-1.3.4d no longer able to authenticate users from Postgresql database So I tried a new version of ProFTPd I was not able to locate lines in universe_wsgi.ini which disable PBKDF2 The answer here does switch the passwords back to SHA1 format: (See http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-September/016749.html ) >>> Ahoj Honzo, >>> >>> Python is case-sensitive. Use 'use_pbkdf2 = False' and make sure you put >>> it under the '[app:main]' section in the config file. >>> >>> Enjoy Galaxy! >>> >>> best >>> >>> Martin Cech

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HTML form of select parameter
by Johannes Eichner 28 Jan '14

28 Jan '14

Dear Galaxy Dev-Team, when using the select parameter in conjunction with options loaded from a text file in the tool_data_path directory (e.g., <options from_file=available_options.txt>) and with the "multiple" attribute set to true, I found that the form of the corresponding HTML widget displayed in the webinterface depends on the number of options listed in the text file. Is there a way to avoid this behaviour in the sense that a fixed HTML form is used independent of the number of available options? It would be great if this was possible, for instance, by changing the value of the display attribute of the select parameter. However, I would also be glad if you could just tell me, where this behaviour of Galaxy is implemented in the source code, such that I can change it according to my needs. Kind regards, Johannes -- Dipl.-Inf. (Bioinf.) Johannes Eichner Univ. Tuebingen, WSI-RA, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071 / 29 78970 Fax: (+49/0) 7071 / 29 5091

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Install tools from Toolshed
by Jennifer Jackson 27 Jan '14

27 Jan '14

Hello Shivani, The problem is either related to 3rd party cookies being enabled or a missing configuration in the universe.wsgi.ini file. This thread, in the second part, provides the full solution: http://dev.list.galaxyproject.org/Invalid-Galaxy-URL-None-Installing-Tools-… Also, make sure you are running the latest version of Galaxy and followed the required upgrade procedures before trying. https://wiki.galaxyproject.org/DevNewsBriefs/ I am moving this over to the galaxy-dev(a)bx.psu.edu mailing list, in case more follow-up is needed. That is the best list to use for troubleshooting local install / tool shed questions. Take care, Jen Galaxy team On 1/25/14 12:36 PM, Malik, Shivani wrote: > HI, > I am trying to install Deseq from the toolshed. I get the > message:Repository installation is not possible due to an invalid > Galaxy URL: *None*. You may need to enable cookies in your browser. > I have enabled the cookies and tried both on Firefox and Chrome but > could not get it to work. Can you help me on this? > Thanks > Shivani > > > ___________________________________________________________ > 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/ > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson http://galaxyproject.org

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The main Galaxy Tool Shed is now running the next-stable branch
by Greg Von Kuster 27 Jan '14

27 Jan '14

The main Galaxy Tool Shed is now running the next-stable branch in preparation for the next Galaxy release tentatively scheduled for 2 weeks from today. The current changeset revision on the main Tool Shed is: changeset: 12285:3fdf673bdfc9 branch: next-stable Complete documentation for all of the new Tool Shed features will be available for the release in 2 weeks, but feel free to check them out now if you want. Here are some of the more prominent new features: 1) The main Tool Shed is now scheduled to run the daily Tool Shed install and test framework, so installation and test results should hopefully be available for most repositories tomorrow. 2) Exporting and importing repository capsules should now be working between tool sheds (e.g., your local Tool Shed and the test Tool Shed, the test Tool Shed and the main Tool Shed, etc.). 3) Repository owners can now authorize others (either users or groups) to administer their repository using the new "Manage repository administrators" option in the Repository Actions pop-up menu. Please report any issues you uncover and we'll get them handled in preparation for the upcoming release. Thanks! Greg Von Kuster

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ProFFTPd-1.3.4d no longer able to authenticate users from Postgresql database
by Hazard, E. Starr 27 Jan '14

27 Jan '14

I was able to query my Postgresql Db for user authentication at one time. I deleted and then rebuilt the postgresql DB and rebuilt the entire Galaxy instance in early December. Since then I cannot get ProFFTPd-1.3.4d to authenticate users from Postgresql database. At that time my existing universe_wsgi.ini I changed the following from postgres to postgresql #database_connection = postgres://galaxy:Galaxy2013@localhost:5434/galaxy_prod database_connection = postgresql://galaxy:galaxy2013@localhost:5434/galaxy_prod What ftp interaction behavior changes were included in this database_connectio method renaming? (And how can I fix them?) My Galaxy users can login to Galaxy just fine and execute programs if I manually load files into the designated FTP dir and then move these to database/files . Screen session from interactive test mode FTP session opened. dispatching PRE_CMD command 'USER [valid email]' to mod_core . . . dispatching CMD command 'PASS (hidden)' to mod_auth no supplemental groups found for user '[valid email]' ROOT PRIVS at mod_auth_pam.c:338 RELINQUISH PRIVS at mod_auth_pam.c:508 mod_sql_passwd/0.4: expected 'PBKDF2$sha256$10000$1xxxxxxxxxx',got Œyyyyyy¹ I am not using either PBKDF2 or sha256 see below why are these prefixes appended? Xxx and yyyy are NOT the same alphanumeric strings SQLLogFile.txt excerpt: Jan 06 17:27:49 mod_sql/4.3[29179]: query "SELECT email,password,' <mailto:'irish(a)musc.edu>[valid email]','{UNKNOWN TAG}',¹/PATH/galaxy-dist/database/files/ <mailto:'/shared/app/Galaxy/galaxy-dist/database/files/irish(a)musc.edu>[vali d email]','/bin/ bash' FROM galaxy_user WHERE email=' <mailto:email='irish(a)musc.edu>[valid email]'" Jan 06 17:27:49 mod_sql/4.3[29179]: entering postgres cmd_close Jan 06 17:27:49 mod_sql/4.3[29179]: connection 'default' count is now 1 Jan 06 17:27:49 mod_sql/4.3[29179]: exiting postgres cmd_close Jan 06 17:27:49 mod_sql/4.3[29179]: exiting postgres cmd_select Jan 06 17:27:49 mod_sql/4.3[29179]: <<< process_named_query 'LookupGalaxyUser' Jan 06 17:27:49 mod_sql/4.3[29179]: <<< sql_lookup Jan 06 17:27:49 mod_sql/4.3[29179]: user UID 0 below SQLMinUserUID 999, using SQLDefaultUID 65533 Jan 06 17:27:49 mod_sql/4.3[29179]: user GID 0 below SQLMinUserGID 999, using SQLDefaultGID 65533 Jan 06 17:27:49 mod_sql/4.3[29179]: cache miss for user ' <mailto:'irish(a)musc.edu>[valid email]' Jan 06 17:27:49 mod_sql/4.3[29179]: user ' <mailto:'irish(a)musc.edu>[valid email]' cached Jan 06 17:27:49 mod_sql/4.3[29179]: + pwd.pw_name : [valid email] Jan 06 17:27:49 mod_sql/4.3[29179]: + pwd.pw_uid : 65533 Jan 06 17:27:49 mod_sql/4.3[29179]: + pwd.pw_gid : 65533 Jan 06 17:27:49 mod_sql/4.3[29179]: + pwd.pw_dir : /PATH/galaxy-dist/database/files/ <mailto:/shared/app/Galaxy/galaxy-dist/database/files/irish@musc.edu>[valid email] Jan 06 17:27:49 mod_sql/4.3[29179]: + pwd.pw_shell : /bin/bash Jan 06 17:27:49 mod_sql/4.3[29179]: <<< cmd_getpwnam Jan 06 17:27:49 mod_sql/4.3[29179]: >>> cmd_auth Jan 06 17:27:49 mod_sql/4.3[29179]: entering postgres cmd_escapestring Jan 06 17:27:49 mod_sql/4.3[29179]: entering postgres cmd_open Jan 06 17:27:49 mod_sql/4.3[29179]: connection 'default' count is now 2 Jan 06 17:27:49 mod_sql/4.3[29179]: exiting postgres cmd_open Jan 06 17:27:49 mod_sql/4.3[29179]: entering postgres cmd_close Jan 06 17:27:49 mod_sql/4.3[29179]: connection 'default' count is now 1 Jan 06 17:27:49 mod_sql/4.3[29179]: exiting postgres cmd_close Jan 06 17:27:49 mod_sql/4.3[29179]: exiting postgres cmd_escapestring Jan 06 17:27:49 mod_sql/4.3[29179]: cache hit for user '[valid email]' Jan 06 17:27:49 mod_sql/4.3[29179]: >>> cmd_check Jan 06 17:27:49 mod_sql/4.3[29179]: checking password using SQLAuthType 'sha1' Jan 06 17:27:49 mod_sql/4.3[29179]: 'sha1' SQLAuthType handler reports failure ProFTPd conf file excerpt: (based on https://wiki.galaxyproject.org/Admin/Config/Upload%20via%20FTP) # Set up mod_sql_password - Galaxy passwords are stored as hex-encoded SHA1 SQLPasswordEngine on SQLPasswordEncoding hex # Set up SQLLogfile SQLLogFile /PATH/ProFFTPd-1.3.4d/etc/SQLLogFile.txt # Set up mod_sql to authenticate against the Galaxy database SQLEngine on SQLBackend postgres SQLConnectInfo galaxy_prod@:5xxx galaxy galpwd # port and password are changed here; they are correct in the working files. SQLAuthTypes SHA1 SQLAuthenticate users # An empty directory in case chroot fails SQLDefaultHomedir /shared/app/ProFFTPd-1.3.4d/default # Define a custom query for lookup that returns a passwd-like entry. UID and GID should match your Galaxy user. SQLUserInfo custom:/LookupGalaxyUser SQLNamedQuery LookupGalaxyUser SELECT "email,password,¹1233¹,'1234',¹/PATH/galaxy-dist/database/files/%U ','/bin/bash' FROM galaxy_user WHERE email='%U'"

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