galaxy-dev July 2012

galaxy-dev@lists.galaxyproject.org

113 participants
168 discussions

RPy and R installation problems
by Chukhman, Morris 16 Jul '12

16 Jul '12

When I try to install rpy-1.0.3 against R-2.11.1 or R-2.15.1 I get the following error about the version number being unobtainable from R --version. python setup.py install --prefix=/path/to/shared/python RHOMES= [] DEBUG= True Setting RHOMES to ['/argus/app/rhel60/R_2.11.1/lib64/R'] Traceback (most recent call last): File "setup.py", line 109, in <module> RVERSION = rpy_tools.get_R_VERSION(RHOME, force_exec=True) File "/argus/app/src/rpy-1.0.3/rpy_tools.py", line 103, in get_R_VERSION raise RuntimeError("Couldn't obtain version number from output\n" RuntimeError: Couldn't obtain version number from output of `R --version'. This is the R --version output: galaxy[rpy-1.0.3]$ R --version R version 2.11.1 (2010-05-31) Copyright (C) 2010 The R Foundation for Statistical Computing ISBN 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under the terms of the GNU General Public License version 2. For more information about these matters see http://www.gnu.org/licenses/. Although rpy2 builds and installs successfully the linear_regression.py module can't seem to use it. It is looking for the rpy module not the rpy2 module. If I ln -s rpy2 rpy, it appears to run but gives an name not defined error in a line like dat= r.list(... What is the proper procedure for installing the R and rpy dependencies? What versions are recommended with the current galaxy on mercurial? On Thu, June 28, 2012 3:51 pm, Susan Hester wrote: > > Hi, > > I'm trying to register in Galaxy on the public server and under the > "user" tab "register" is greyed out? How do I register? > > Susan Hester, Ph.D. > Research Biologist > Systems Biology Branch > Integrated Systems Toxicology Division (ISTD) > National Health and Environmental Effects Research Lab > US Environmental Protection Agency > 109 T.W. Alexander Dr. > MD-B143-06 > Research Triangle Park, NC 27711 > hester.susan(a)epa.gov___________________________________________________________ > 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/

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fonction
by VICTORIA SPARTACUS 16 Jul '12

16 Jul '12

Hello, I want to know if I can do something on galaxy. I have a folder for the chromosome 1 with start of G4 and start of ORI. For each start G4 I associated all of start ORI. For example if I have 2 start G4 (2 lines) and 4 start ORI (2 lines), I will have on a new file 8 lines. startG4-1 start ORI-1 startGA-1 startORI-2 startG4-1 startORI-3 startG4-1 startORI-4 startG4-2 startORI-1 startG4-2 starORI-2 startG4-2 startORI-3 startG4-2 startORI-4 Now I do the difference between the first column and the second and I want the absolute value of this difference to have the distance between the start G4 and the start ORI. I obtain a third column. Now that I want is the minimum of those absolute values. And I want to know which start G4 and which start ORI who correspond to this mimnimum. For example if the minimum of startG4-1 is on the third column and the minimum of startG4-2 is on the second column. I want as result startG4-1 startORI-3 min(c2-c1) startG4-2 startORI-2 min(c2-c1) So know my question is, do you know if I can obtain that I wnt on Galaxy, and if YES how? Best regards, Victoria Spartacus

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Re: [galaxy-dev] Configuring FastQC to run
by Klaus Metzeler 15 Jul '12

15 Jul '12

Peter: GAlaxy is looking for the FastQC executable at the following location (see last line of error message): /opt/galaxy/galaxy-dist/tool-data/shared/jars/FastQC/fastqc You wrote that the fastqc binary is somewhere in Galaxy's $PATH, but is it really in the above directory? If not, try moving the fastqc executable there (or create a symlink) and it should work. Best, Klaus >> >

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Restore Account
by Ming Yu 14 Jul '12

14 Jul '12

Hello, My Galaxy account leonyuming(a)gmail.com has been marked deleted. Would you please restore it for me? Thank you very much. Best, Leon

2 1

pbs_python issues
by Iry Witham 13 Jul '12

13 Jul '12

I am having an issue with pbs_python loading, but not submitting jobs to the cluster. The first issue is that when I ran 'LIBTORQUE_DIR=/usr/local/lib/ python scripts/scramble.py –e pbs_python' it failed to generate the pbs_python egg in the /galaxy-dist/eggs/ directory. Secondly I copied the pbs_python-4.1.0-py2.6-linux-x86_64-ucs4.egg from my production galaxy server and restarted my test server. It appears to start, but when I attempt to run anything it uses the local runner and fails. The runner0.log shows the pbsjobrunner is loaded is below: galaxy.jobs.handler DEBUG 2012-07-06 10:08:45,681 Loaded job runner: galaxy.jobs.runners.pbs:PBSJobRunner galaxy.jobs.handler INFO 2012-07-06 10:08:45,682 job handler stop queue started galaxy.jobs.manager INFO 2012-07-06 10:08:45,687 job manager queue started galaxy.jobs.manager INFO 2012-07-06 10:08:45,688 job manager stop queue started galaxy.jobs.handler INFO 2012-07-06 10:08:45,692 job handler queue started I can't seem to get past this point since I upgraded. Can someone point me in the right direction? Thanks, Iry The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.

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Re: [galaxy-dev] Setting up proftpd problem: ftp login failure
by Joachim Jacob 13 Jul '12

13 Jul '12

Alex, Thanks for the assistance! The modules work fine, since i see them in the log files. The id and gid match the output of id galaxy. I think the problem lies somewhere else. Kind regards Joachim "Bossers, Alex" <Alex.Bossers(a)wur.nl>schreef: >Joachim, >If I remember correctly for our galaxy proftpd setup on ubuntu 10.10. >Be sure to compile proftpd with the required additional SQL modules. > >Then figure out the user and group ids of galaxy user that can access the DB (mysql in our case). >$ id galaxy (or whatever user you use) > >Make sure these ids are in the SELECT statement of the proftpd config file >Below our section: > ># 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,'1001','1002','/mnt/galaxy_data/galaxy_database/ftp/%U','/bin/bash' FROM galaxy_user WHERE email='%U'" > >In our case de uid and gid were 1001 and 1002 > >Hope it helps, >Alex > > >-----Oorspronkelijk bericht----- >Van: galaxy-dev-bounces(a)lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] Namens Joachim Jacob >Verzonden: vrijdag 13 juli 2012 15:19 >Aan: galaxy-dev(a)lists.bx.psu.edu >Onderwerp: [galaxy-dev] Setting up proftpd problem: ftp login failure > >Dear Galaxy devs, > >I am setting up an ftp server with authentication to the Galaxy user tables, but the password is not recognized as being correct. > >joachim@joachim-laptop:~$ ftp 192.168.10.23 Connected to 192.168.10.23. >220 Welcome to BITS Galaxy FTP server. >Name (192.168.10.23:joachim): joachim.jacob(a)vib.be >331 Password required for joachim.jacob(a)vib.be >Password: >530 Login incorrect. >Login failed. >421 Service not available, remote server has closed connection >ftp> > > >My setup: >- Centos 6.2 >- proftpd 1.3.3 >- postgres (PostgreSQL) 8.4.11 > >I have configured proftpd.conf (see below), and also /var/lib/pgsql/data/pg_hba.conf. > >*** proftpd.conf *** ># This is the ProFTPD configuration file # Server Config - config used for anything outside a <VirtualHost> or <Global> context > >ServerName "BITS Galaxy FTP" >ServerIdent on "Welcome to BITS Galaxy FTP server." >ServerType standalone >ServerAdmin root@localhost >DefaultServer on >Port 21 >Umask 077 >SyslogFacility DAEMON >SyslogLevel debug >DefaultRoot ~ !adm >CreateHome on dirmode 700 >PassivePorts 39000 40000 >MaxInstances 30 >User nobody >Group nobody > ># Don't do reverse DNS lookups (hangs on DNS problems) >UseReverseDNS off >MaxInstances 20 > ># Define the log formats >LogFormat default "%h %l %u %t \"%r\" %s %b" >LogFormat auth "%v [%P] %h %t \"%r\" %s" > ># General database support >LoadModule mod_sql.c > ># Support for base-64 or hex encoded MD5 and SHA1 passwords from SQL tables LoadModule mod_sql_passwd.c > ># Postgresql support (requires proftpd-postgresql package) LoadModule mod_sql_postgres.c > ><Global> > # Allow users to overwrite files and change permissions > AllowOverwrite yes > AllowStoreRestart on > > # Bar use of SITE CHMOD > <Limit SITE_CHMOD> > DenyAll > </Limit> > > # Bar use of RETR (download) since this is not a public file drop > <Limit RETR> > DenyAll > </Limit> > > SQLLogFile /var/log/proftpd/proftpd.log > > # Set up mod_sql_password - Galaxy passwords are stored as hex-encoded SHA1 > SQLPasswordEngine on > SQLPasswordEncoding hex > RequireValidShell off > # Set up mod_sql to authenticate against the Galaxy database > SQLEngine on > SQLBackend postgres > SQLConnectInfo galaxydb(a)127.0.0.1 ftpuser ftppassword > SQLAuthTypes SHA1 > SQLAuthenticate users > > # An empty directory in case chroot fails > SQLDefaultHomedir /mnt/galaxytemp/ftptmp > SQLMinID 98 > # 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,'600','601','/mnt/galaxydb/ftp/%U','/bin/bash' FROM galaxy_user WHERE email='%U'" ></Global> > > >Now upon trying to connect with ftp to the server, it fails prompting >that the login is incorrect (tried also from outside our network, also >using FileZilla): > >joachim@joachim-laptop:~$ ftp 192.168.10.23 >Connected to 192.168.10.23. >220 Welcome to BITS Galaxy FTP server. >Name (192.168.10.23:joachim): joachim.jacob(a)vib.be >331 Password required for joachim.jacob(a)vib.be >Password: >530 Login incorrect. >Login failed. >421 Service not available, remote server has closed connection >ftp> > > >The lengthy log of proftpd has this logged: > >Jul 13 14:30:56 mod_sql/4.2.5[23479]: defaulting to 'postgres' backend >Jul 13 14:30:56 mod_sql/4.2.5[23479]: backend module >'mod_sql_postgres/4.0.4' >Jul 13 14:30:56 mod_sql/4.2.5[23479]: backend api 'mod_sql_api_v1' >Jul 13 14:30:56 mod_sql/4.2.5[23479]: >>> sql_sess_init >Jul 13 14:30:56 mod_sql/4.2.5[23479]: entering postgres >cmd_defineconnection >Jul 13 14:30:56 mod_sql/4.2.5[23479]: name: 'default' >Jul 13 14:30:56 mod_sql/4.2.5[23479]: user: 'galaxyftp' >Jul 13 14:30:56 mod_sql/4.2.5[23479]: host: '127.0.0.1' >Jul 13 14:30:56 mod_sql/4.2.5[23479]: db: 'galaxydb' >Jul 13 14:30:56 mod_sql/4.2.5[23479]: port: '5432' >Jul 13 14:30:56 mod_sql/4.2.5[23479]: ttl: '0' >Jul 13 14:30:56 mod_sql/4.2.5[23479]: exiting postgres >cmd_defineconnection >Jul 13 14:30:56 mod_sql/4.2.5[23479]: mod_sql engine : on >Jul 13 14:30:56 mod_sql/4.2.5[23479]: negative_cache : off >Jul 13 14:30:56 mod_sql/4.2.5[23479]: authenticate : users >Jul 13 14:30:56 mod_sql/4.2.5[23479]: usertable : users >Jul 13 14:30:56 mod_sql/4.2.5[23479]: userid field : userid >Jul 13 14:30:56 mod_sql/4.2.5[23479]: password field : passwd >Jul 13 14:30:56 mod_sql/4.2.5[23479]: UID field : uid >Jul 13 14:30:56 mod_sql/4.2.5[23479]: GID field : gid >Jul 13 14:30:56 mod_sql/4.2.5[23479]: homedir field : homedir >Jul 13 14:30:56 mod_sql/4.2.5[23479]: homedir(default) : >'/mnt/galaxytemp/ftptmp' >Jul 13 14:30:56 mod_sql/4.2.5[23479]: shell field : shell >Jul 13 14:30:56 mod_sql/4.2.5[23479]: SQLMinUserUID : 98 >Jul 13 14:30:56 mod_sql/4.2.5[23479]: SQLMinUserGID : 98 >Jul 13 14:30:56 mod_sql/4.2.5[23479]: <<< sql_sess_init >Jul 13 14:31:14 mod_sql/4.2.5[23479]: >>> sql_pre_pass >Jul 13 14:31:14 mod_sql/4.2.5[23479]: <<< sql_pre_pass >Jul 13 14:31:14 mod_sql/4.2.5[23479]: >>> cmd_getpwnam >Jul 13 14:31:14 mod_sql/4.2.5[23479]: entering postgres cmd_escapestring >Jul 13 14:31:14 mod_sql/4.2.5[23479]: entering postgres cmd_open >Jul 13 14:31:14 mod_sql/4.2.5[23479]: Postgres server version: 8.4.11 >Jul 13 14:31:14 mod_sql/4.2.5[23479]: Postgres connection character set >now 'UTF8' (from 'UTF-8 >') >Jul 13 14:31:14 mod_sql/4.2.5[23479]: connection 'default' opened >Jul 13 14:31:14 mod_sql/4.2.5[23479]: connection 'default' count is now 2 >Jul 13 14:31:14 mod_sql/4.2.5[23479]: exiting postgres cmd_open >Jul 13 14:31:14 mod_sql/4.2.5[23479]: entering postgres cmd_close >Jul 13 14:31:14 mod_sql/4.2.5[23479]: connection 'default' count is now 1 >Jul 13 14:31:14 mod_sql/4.2.5[23479]: exiting postgres cmd_close >Jul 13 14:31:14 mod_sql/4.2.5[23479]: exiting postgres cmd_escapestring >Jul 13 14:31:14 mod_sql/4.2.5[23479]: cache miss for user >'joachim.jacob(a)vib.be' >Jul 13 14:31:14 mod_sql/4.2.5[23479]: >>> sql_lookup >Jul 13 14:31:14 mod_sql/4.2.5[23479]: >>> process_named_query >'LookupGalaxyUser' >Jul 13 14:31:14 mod_sql/4.2.5[23479]: entering postgres cmd_escapestring >Jul 13 14:31:14 mod_sql/4.2.5[23479]: entering postgres cmd_open >Jul 13 14:31:14 mod_sql/4.2.5[23479]: connection 'default' count is now 2 >Jul 13 14:31:14 mod_sql/4.2.5[23479]: exiting postgres cmd_open >Jul 13 14:31:14 mod_sql/4.2.5[23479]: entering postgres cmd_close >Jul 13 14:31:14 mod_sql/4.2.5[23479]: connection 'default' count is now 1 >Jul 13 14:31:14 mod_sql/4.2.5[23479]: exiting postgres cmd_close >Jul 13 14:31:14 mod_sql/4.2.5[23479]: exiting postgres cmd_escapestring >Jul 13 14:31:14 mod_sql/4.2.5[23479]: entering postgres cmd_select >Jul 13 14:31:14 mod_sql/4.2.5[23479]: entering postgres cmd_open >Jul 13 14:31:14 mod_sql/4.2.5[23479]: connection 'default' count is now 2 >Jul 13 14:31:14 mod_sql/4.2.5[23479]: exiting postgres cmd_open >Jul 13 14:31:14 mod_sql/4.2.5[23479]: query "SELECT >email,password,'600','601','/mnt/galaxydb/ftp/joachim.jacob(a)vib.be','/bin/bash' >FROM galaxy_user WHERE email='joachim.jacob(a)vib.be'" >Jul 13 14:31:14 mod_sql/4.2.5[23479]: entering postgres cmd_close >Jul 13 14:31:14 mod_sql/4.2.5[23479]: connection 'default' count is now 1 >Jul 13 14:31:14 mod_sql/4.2.5[23479]: exiting postgres cmd_close >Jul 13 14:31:14 mod_sql/4.2.5[23479]: exiting postgres cmd_select >Jul 13 14:31:14 mod_sql/4.2.5[23479]: <<< process_named_query >'LookupGalaxyUser' >Jul 13 14:31:14 mod_sql/4.2.5[23479]: <<< sql_lookup >Jul 13 14:31:14 mod_sql/4.2.5[23479]: cache miss for user >'joachim.jacob(a)vib.be' >Jul 13 14:31:14 mod_sql/4.2.5[23479]: user 'joachim.jacob(a)vib.be' cached >Jul 13 14:31:14 mod_sql/4.2.5[23479]: + pwd.pw_name : joachim.jacob(a)vib.be >Jul 13 14:31:14 mod_sql/4.2.5[23479]: + pwd.pw_uid : 600 >Jul 13 14:31:14 mod_sql/4.2.5[23479]: + pwd.pw_gid : 601 >Jul 13 14:31:14 mod_sql/4.2.5[23479]: + pwd.pw_dir : >/mnt/galaxydb/ftp/joachim.jacob(a)vib.be >Jul 13 14:31:14 mod_sql/4.2.5[23479]: + pwd.pw_shell : /bin/bash >Jul 13 14:31:14 mod_sql/4.2.5[23479]: <<< cmd_getpwnam >Jul 13 14:31:14 mod_sql/4.2.5[23479]: >>> cmd_auth >Jul 13 14:31:14 mod_sql/4.2.5[23479]: entering postgres cmd_escapestring >Jul 13 14:31:14 mod_sql/4.2.5[23479]: entering postgres cmd_open >Jul 13 14:31:14 mod_sql/4.2.5[23479]: connection 'default' count is now 2 >Jul 13 14:31:14 mod_sql/4.2.5[23479]: exiting postgres cmd_open >Jul 13 14:31:14 mod_sql/4.2.5[23479]: entering postgres cmd_close >Jul 13 14:31:14 mod_sql/4.2.5[23479]: connection 'default' count is now 1 >Jul 13 14:31:14 mod_sql/4.2.5[23479]: exiting postgres cmd_close >Jul 13 14:31:14 mod_sql/4.2.5[23479]: exiting postgres cmd_escapestring >Jul 13 14:31:14 mod_sql/4.2.5[23479]: cache hit for user >'joachim.jacob(a)vib.be' >Jul 13 14:31:14 mod_sql/4.2.5[23479]: >>> cmd_check >Jul 13 14:31:14 mod_sql/4.2.5[23479]: checking password using >SQLAuthType 'sha1' >Jul 13 14:31:14 mod_sql/4.2.5[23479]: 'sha1' SQLAuthType handler reports >success >Jul 13 14:31:14 mod_sql/4.2.5[23479]: cache hit for user >'joachim.jacob(a)vib.be' >Jul 13 14:31:14 mod_sql/4.2.5[23479]: <<< cmd_check >Jul 13 14:31:14 mod_sql/4.2.5[23479]: <<< cmd_auth >Jul 13 14:31:14 mod_sql/4.2.5[23479]: >>> cmd_getpwnam >Jul 13 14:31:14 mod_sql/4.2.5[23479]: cache hit for user >'joachim.jacob(a)vib.be' >Jul 13 14:31:14 mod_sql/4.2.5[23479]: <<< cmd_getpwnam >Jul 13 14:31:14 mod_sql/4.2.5[23479]: entering postgres cmd_exit >Jul 13 14:31:14 mod_sql/4.2.5[23479]: entering postgres cmd_close >Jul 13 14:31:14 mod_sql/4.2.5[23479]: connection 'default' closed >Jul 13 14:31:14 mod_sql/4.2.5[23479]: connection 'default' count is now 0 >Jul 13 14:31:14 mod_sql/4.2.5[23479]: exiting postgres cmd_close >Jul 13 14:31:14 mod_sql/4.2.5[23479]: exiting postgres cmd_exit > >So a lot of exiting here. Can anybody help me further with this? > >Have a pleasant weekend! > > >Joachim > >-- >Joachim Jacob, PhD > >Rijvisschestraat 120, 9052 Zwijnaarde >Tel: +32 9 244.66.34 >Bioinformatics Training and Services (BITS) >http://www.bits.vib.be >@bitsatvib > >___________________________________________________________ >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/ > > > >

1 0

List of browsers which supports galaxy
by sshashi 13 Jul '12

13 Jul '12

Hi, some browser are not supporting galaxy. if galaxy is supporting to specific version of browser in mozila ,IE,chrome,safari etc , can i get version number in mozila ,IE,chrome? if i have downloaded any new version of galaxy ,where will i get the list of supporting browser ? Regards shashi ------------------------------------------------------------------------------------------------------------------------------- This e-mail is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies and the original message. Any unauthorized review, use, disclosure, dissemination, forwarding, printing or copying of this email is strictly prohibited and appropriate legal action will be taken. -------------------------------------------------------------------------------------------------------------------------------

4 4

Ability to Select SGE queue?
by Moore, Raymond M. 13 Jul '12

13 Jul '12

I'd like to provide a choice to my users which size Queue they would like to use when they are about to run a tool. I'm using the SGE configuration through DRMAA on my local install. I've only seen the queue set in the wsgi.ini file. Is there a way I can include this choice of SGE queue in my xml? Thanks Raymond Moore Informatics Specialist, Division of Biomedical Statistics & Informatics | 507-293-0054 Mayo Clinic | 200 First Street SW | Rochester, MN 55905 | www.mayoclinic.org <http://www.mayoclinic.org/>

3 3

How to make trackster jobs run locally instead of on a cluster?
by Dorset, Daniel C 13 Jul '12

13 Jul '12

We have an instance of Galaxy deployed on a local institutional cluster. It's working well, but when we import BED files for visualization, Galaxy runs the processing for these on the cluster. I would like to run these tasks locally instead. I understand how to make individual tools run locally, but I'm hoping there's a better way to accomplish what I would like to do without having to specify each of the many conversion tools individually in the universe_wsgi.ini config file. Thanks! Dan

2 1

Configuring FastQC to run
by Peter Schmitt 13 Jul '12

13 Jul '12

I get the following error when attempting to run FastQC from galaxy: job command line: python /opt/galaxy/galaxy-dist/tools/rgenetics/rgFastQC.py -i /opt/galaxy/galaxy-dist/database/files/000/dataset_75.dat -d /opt/galaxy/galaxy-dist/database/job_working_directory/000/114/dataset_128_files -o /opt/galaxy/galaxy-dist/database/files/000/dataset_128.dat -n "FastQC" -f fastqsanger -j SRS280832_1_FASTQ Groomer on data 14 -e /opt/galaxy/galaxy-dist/tool-data/shared/jars/FastQC/fastqc ----------------------------------------------------------------------------- job stderr: Traceback (most recent call last): File "/opt/galaxy/galaxy-dist/tools/rgenetics/rgFastQC.py", line 149, in<module> assert os.path.isfile(opts.executable),'##rgFastQC.py error - cannot find executable %s' % opts.executable AssertionError: ##rgFastQC.py error - cannot find executable /opt/galaxy/galaxy-dist/tool-data/shared/jars/FastQC/fastqc The fastqc binary is in galaxy's PATH. Any help would be appreciated. -- * *

2 1

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galaxy-dev July 2012