June 2013 - galaxy-dev - lists.galaxyproject.org

[GSoC2013] Week 1 Accomplishments and Week 2 Plans
by Saket Choudhary 24 Jun '13

24 Jun '13

Hi Everyone, Just wrote a blog post for my Week1 tasks and Week 2 to-dos: http://galaxy-gsoc2013.blogspot.in/2013/06/week-1-accomplishments-and-week-… I am maintaining a work log in this doc : https://docs.google.com/document/d/1VCKCpKW6C_Tt1DYWi43GAN_Jo-nebkkj8Ctq7WL… If you have any suggestions for the VCF4.1 issue or otherwise. please do let me know. Thanks Saket Choudhary Undergraduate Dept. of Chemical Engineering IIT Bombay

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Re: [galaxy-dev] [galaxy-user] Problems when downloading a local galaxy tool (old version)
by Dannon Baker 23 Jun '13

23 Jun '13

Hsiong, Could you try 'hg clone --verbose --debug https://bitbucket.org/galaxy/galaxy-dist/' to see if we get more useful error output? If it passed the warning and went ahead and got all the changes then I'm not sure if that's an issue. Also, I'm swapping this thread to the galaxy-dev list, since it's about installing a local instance. -Dannon On Sun, Jun 23, 2013 at 1:15 AM, xiong <lynhsiong(a)hotmail.com> wrote: > ** > Dear friends: > > As a locally installed Genomic-hyperbrowser need a rather old > version of Galaxy, I runed the command "hg clone > https://bitbucket.org/galaxy/galaxy-dist/ -u 26920e20157f galaxy-dist-hb" > according to the website > http://hyperbrowser.uio.no/hb/static/download.html. However, the hg did > not download successfully, but reported > > "warning: bitbucket.org certificate with fingerprint > 24:9c:45:8b:9c:aa:ba:55:4e:01:6d:58:ff:e4:28:7d:2a:14:ae:3b not verified > (check hostfingerprints or web.cacerts config setting) > destination directory: galaxy-dist-hb > requesting all changes > adding changesets" > > and this information on the screen mainteined (at least half a day unless > I hit "ctrl+Z" and kill the job) without any other errors (still in the > destination directory it generated a nearly empty dir > "galaxy-dist-hb" containing a filefold named ".hg”——one "store" filefold > and several small files included). My mercurial version is 2.6, and I use > Xshell to reach CentOS Server. > > Actually, even I downloaded the latest version of galaxy (hg clone > https://bitbucket.org/galaxy/galaxy-dist/) it also reported the same > information on the screen. > On the other hand, I can get the latest tarballs of galaxy, but > it can not be updated to an old version. > > Please give me some clues about problems above, and any ideas to get > tarballs for an old version? > > Thanks in advance! > > Hsiong > > ___________________________________________________________ > 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/ >

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Profile loss
by Marley Yeong 22 Jun '13

22 Jun '13

Dear sir or madam, It seems my profile has been deleted, before galaxy went offline (about two weeks ago) I made a profile with the email address: marleyyeong(a)live.nl.I keep getting the "no such user" error. And I'm pretty sure the login information is typed correctly.It stored a school project, so any help would be greatly appreciated. Thanks in advance, Marley Yeong

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Re: [galaxy-dev] Portable tool identifiers in workflows
by Peter Cock 22 Jun '13

22 Jun '13

On Thu, Jun 13, 2013 at 6:34 PM, Greg Von Kuster <greg(a)bx.psu.edu> wrote: > Hello Peter, > > Unfortunately, workflows are currently not very compatible with > the tool shed - there is a Trello card that details the issues here: > > https://trello.com/card/workflow-issues/506338ce32ae458f6d15e4b3/692 > Thanks Greg - I see that Trello card is "in progress", but it covers quite a broad range of issues. >> So, does Galaxy handle old fashioned tool identifiers and the >> newer toolshed-tool-identifiers gracefully in a situation like this? > > Unfortunately this does not currently work ... > >> Do I need to update the *.ga files to use toolshed-tool-ids? If >> I did that, would it break the workflow on any Galaxy instance >> (like ours) where the tools were installed manually? > > Yes, you would currently need to update the workflows to use > toolshed-tool-ids, and your statement regarding the workflow > not working with older tools is correct. So in the short term the best thing to do is to edit these workflows as posted on the Tool Shed (easy enough as the *.ga files are plain text) to replace the tool identifiers? What would be the easiest way to work out the desired id form from a tool repository page? Other than reinstalling the tools locally but from the Tool Shed this time? ;) Thanks, Peter

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Re: [galaxy-dev] ProFTPD integration with Galaxy
by Perez, Ricardo 21 Jun '13

21 Jun '13

Hi Mr. Tobias, We are having a similar problem. It seems that when the galaxy code was updates, new created/updated passwords are using a different encryption mode. This new mode, PBKDF2 SHA256 is NOT supported by proftpd 1.3.4d that you see to be using. We had to compile proftpd from source since version 1.3.5rc3 does support this encryption. Now in the password PBKDF2$sha256$10000$8h/4HmD1Eu6NTc7F$Slb1H5a9YJvR6A3cUnZCUfh7tOWKfRuh I was able to deduce the following by reading the code from git hub "password.py". The encrypted password is acually Slb1H5a9YJvR6A3cUnZCUfh7tOWKfRuh where the salt is 8h/4HmD1Eu6NTc7F using PBKDF2 SHA256 with an illiteration value of 10000. The most importnat part is that the salt, is right there, from character 21 to 36. With the newly compiled proftpd, I have the following configuration at proftpd.conf: # This is a basic ProFTPD configuration file (rename it to # 'proftpd.conf' for actual use. It establishes a single server # and a single anonymous login. It assumes that you have a user/group # "nobody" and "ftp" for normal operation and anon. ServerName "Genomics01 ProFTPd" ServerType standalone DefaultServer on DeferWelcome off UseIPv6 on IdentLookups off MultilineRFC2228 on ShowSymlinks on ModulePath /usr/local/galaxy/downloads/proftpd-1.3.5rc3/modules/ LoadModule mod_sql.c LoadModule mod_sql_postgres.c LoadModule mod_sql_passwd.c <IfModule mod_sql.c> SQLBackend postgres SQLEngine on SQLAuthenticate users SQLAuthTypes SHA1 SHA256 pbkdf2 SQLPasswordPBKDF2 SHA256 1000 24 #SQLPasswordSaltFile /path/to/file SQLConnectInfo galaxydb@localhost:5432 ftpuser mypassword SQLUserInfo custom:/LookupGalaxyUser SQLNamedQuery LookupGalaxyUser SELECT "email,password,'galaxy','galaxy','/usr/local/galaxy/galaxy-dist/database/ftp/%U','/bin/bash' FROM galaxy_user WHERE email='%U'" SQLPasswordUserSalt sql:/GetUserSalt SQLNamedQuery LookupGalaxyUser SELECT "email, (CASE WHEN substring(password from 1 for 6) = 'PBDKF2' THEN substring(password from 38 for 69) ELSE password END) AS password2,'galaxy','galaxy','/usr/local/galaxy/galaxy-dist/database/ftp/%U','/bin/bash' FROM galaxy_user WHERE email='%U'" SQLNamedQuery GetUserSalt SELECT "(CASE WHEN SUBSTRING (password from 1 for 6) = 'PBDKF2' THEN SUBSTRING (password from 21 for 36) END) AS salt FROM galaxy_user WHERE email='%U'" </IfModule> SQLDefaultGID 1002 SQLDefaultUID 1002 TimeoutNoTransfer 600 TimeoutStalled 600 TimeoutIdle 1200 DisplayLogin welcome.msg DisplayChdir .message true ListOptions "-l" DenyFilter \*.*/ # Use this to jail all users in their homes DefaultRoot ~ CreateHome on dirmode 700 AllowOverwrite on AllowStoreRestart on SQLPasswordEngine on SQLPasswordEncoding hex PassivePorts 30000 40000 # Port 21 is the standard FTP port. Port 21 # Don't use IPv6 support by default. # Umask 022 is a good standard umask to prevent new dirs and files # from being group and world writable. Umask 077 # To prevent DoS attacks, set the maximum number of child processes # to 30. If you need to allow more than 30 concurrent connections # at once, simply increase this value. Note that this ONLY works # in standalone mode, in inetd mode you should use an inetd server # that allows you to limit maximum number of processes per service # (such as xinetd). MaxInstances 30 # Set the user and group under which the server will run. User galaxy Group galaxy # To cause every FTP user to be "jailed" (chrooted) into their home # directory, uncomment this line. #DefaultRoot ~ # Normally, we want files to be overwriteable. AllowOverwrite on #AuthOrder mod_sql.c # Bar use of SITE CHMOD by default #<Limit SITE_CHMOD> # DenyAll #</Limit> Include /etc/proftpd/conf.d/ With the configuration above, I can still connect to users that have SHA1 passwords, but I think I need a little more tweeking to get it to work with the new passwords. Best, --Ricardo Perez

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Installation of 20130603 Galaxy image with MySQL fails
by Linda Cham 21 Jun '13

21 Jun '13

Hi. I am new to the Galaxy forum and I am trying to setup a new local Galaxy instance with MySQL on RH6.2 x86_64. On a newly installed OS node, using the hg clone command (hg clone https://bitbucket.org/galaxy/galaxy-dist#stable) which gets the current Galaxy 20130603 image, I am getting the following errors when running run.sh: File "build/bdist.linux-x86_64-ucs4/egg/MySQLdb/cursors.py", line 173, in execute self.errorhandler(self, exc, value) File "build/bdist.linux-x86_64-ucs4/egg/MySQLdb/connections.py", line 36, in defaulterrorhandler raise errorclass, errorvalue OperationalError: (OperationalError) (1170, "BLOB/TEXT column 'slug' used in key specification without a key length") 'CREATE INDEX ix_history_slug ON history (slug)' () Reading the forum, someone stated it can be bypass by running the CREATE INDEX. mysql> CREATE INDEX ix_history_slug ON history (slug(1000)); Query OK, 0 rows affected (0.09 sec) Records: 0 Duplicates: 0 Warnings: 0 When trying to run.sh again after the CREATE INDEX, will get this error: File "/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/lib/galaxy/app.py", line 52, in __init__ create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get ( '__file__', None ), self.config.database_engine_options, app=self ) File "/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/lib/galaxy/model/migrate/check.py", line 107, in create_or_verify_database % ( db_schema.version, migrate_repository.versions.latest, config_arg ) ) Exception: Your database has version '29' but this code expects version '115'. Please backup your database and then migrate the schema by running 'sh manage_db.sh upgrade'. So try to run the "sh manage_db.sh upgrade' now will get this error: $ sh manage_db.sh upgrade Traceback (most recent call last): File "./scripts/manage_db.py", line 13, in <module> from migrate.versioning.shell import main File "/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/shell.py", line 12, in <module> from migrate.versioning import api File "/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/api.py", line 33, in <module> from migrate.versioning import (repository, schema, version, File "/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/repository.py", line 13, in <module> from migrate.versioning import version, pathed, cfgparse File "/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/version.py", line 10, in <module> from migrate.versioning import pathed, script File "/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/pathed.py", line 11, in <module> from migrate.versioning.util import KeyedInstance File "/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/util/__init__.py", line 7, in <module> from decorator import decorator ImportError: No module named decorator In some searches, there were tips of deleting the eggs directory and rerun run.sh or use a python env. Neither option worked. Was not able to find anything meaningful about the decorator error. Note:, I was able to get Galaxy up with MySQL using the Galaxy 788cd3d06541 image on a different node. So I am thinking maybe it is the new 20130603 image that is giving me issues? Commands used to get Galaxy up: Install mysql from yum repository [MySQL 5.1.52-1.el6_0.1] python version [2.6.6] Grant ALL PRIVILEGES galaxy_db.* TO galaxy_user on localhostname with PWD Images tested: *Copy of the galaxy-galaxy-dist-788cd3d06541.tar.bz2 image Did not run the hg update command. [This worked] *hg clone stable of newest image [Failed] Update the universe_wsg.ini with the port, host, database_connection to mysql Ran run.sh Thanks. Linda

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nglims roles
by Lee Katz 21 Jun '13

21 Jun '13

Hi, what roles are embedded in nglims? (am I calling it by the right name?) I have a "sequencing" role which will be given to anyone submitting a request, and that seems to be working just fine. I am also using the yaml form to edit the submission form, and I think it's beautifully implemented. However, I cannot figure out how someone on our MiSeq team will access the submissions unless they are admins of Galaxy. I would like to avoid this situation because the MiSeq team should not have the same permissions that allows them to view all data or install new tools. Is there a role that I can give someone who is actually performing the sequencing? And what would it be? -- Lee Katz, Ph.D.

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visulaization tool
by shashi shekhar 21 Jun '13

21 Jun '13

Hi, i want to add new visualization tool in galaxy . can i get the required documents ? can u send me the details how can i add the visualization tool in galaxy . Regards shashi

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Initial display with Simulate (version 1.0.0)
by Perez, Ricardo 20 Jun '13

20 Jun '13

Dear all, When running Simulate (version 1.0.0)I am missing a graph in the initial display. Is this a bug or is it my instance problem. On a side note, when running Simulate I found out that if you don't place parameters in "Frequency/ies for minor allele:" and "Detection thresholds:" the job will fail. It would be nice to indicate that those parameters are a must for running the tool. Thank you, --Ricardo Perez

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simplest way to connect RNAseq tools for a local Galaxy instance
by Elwood Linney 20 Jun '13

20 Jun '13

I have: 1) downloaded the Galaxy framework into a Mac Pro desktop with 64gb ram 2) downloaded Mac OS versions of Tophat2, Bowtie2, and the Cufflink suite to the mac 3) have looked at the Galaxy wiki on connecting these [http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies] 4) I have gotten some useful advice from Dannon Baker on how to introduce my large datasets on the some computer into Galaxy through Admin changing some permissions but my minimal knowledge of unix commands and tricks has me stymied Question: If my primary purpose is to use this local instance for the analysis of RNAseq data within my lab, what is the simplest way of connecting the programs to the Galaxy framework? While from reviewing info on the Galaxy website I am only guessing that adding them to $PATH might be the easiest way for me to do this (but I am not exactly sure what this means or specifically how I would do it in my case). However, I do initiate the running of Galaxy by sh run.sh on my terminal and visualizing things via my localhost port. There is some indication from the wiki I found that this might not be good for a system initiated by sh run.sh . [http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies] under "Local Jobs" I would appreciate any specific advice on this. Sincerely, Elwood Linney DUMC

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