July 2012 - galaxy-dev - lists.galaxyproject.org

Setting up proftpd problem: ftp login failure
by Joachim Jacob 13 Jul '12

13 Jul '12

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

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Re: [galaxy-dev] Configuring a ProFTPd server for Galaxy
by Joachim Jacob 13 Jul '12

13 Jul '12

Hi Geoff, I encountered the same issue configuring proftpd - thanks for mentioning this issue. Would you mind sharing how you exactly solved the issue with the uid/gid of the galaxy user? I want not to change the uid/gid of this user as it is the same on other machines here. Joachim ------------------------------ Message: 1223 Date: Wed, 9 Feb 2011 11:31:56 -0800 (PST) From: Geoff Jentry<geoffjentry(a)hexdump.org> To:galaxy-dev@bx.psu.edu Subject: Re: [galaxy-dev] Configuring a ProFTPd server for Galaxy Message-ID: <Pine.LNX.4.64.1102091130490.18757(a)cardinals.dreamhost.com> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Oops, please disregard. As luck would have it, the moment I throw in the towel the answer becomes obvious to me. The uid/gid for my galaxy user was below 999 and getting bumped up to 65535 by the SQL authentication, so the user FTP directory was getting that uid/gid, was not writeable and it'd bomb out. Works now. On Wed, 9 Feb 2011, Geoff Jentry wrote: > This is probably more appropriate for the proftpd list at this point, but my > thought is that maybe someone has come across this while configuring a > proftpd server for galaxy usage. I'm including my current output when I try > to log on, a copy of my conf file, and output from the SQL log (in all three > cases, with identifying info removed - users, hosts, IPs, etc). > > You can see from the SQL Log that it appears the log in is actually > successful, but then the connection simply closes the connection. Any ideas > as to what I've got configured incorrectly here? -- Joachim Jacob, PhD Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib

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Galaxy fails to start after shut down
by Joachim Jacob 13 Jul '12

13 Jul '12

Dear Galaxy Devs, After a power shutdown of our machines, Galaxy starts up with serving on localhost:8080 (according to paster.log), but I get an error upon requesting the webpage: SyntaxError: invalid syntax (base_panels.mako.py, line 301) URL: http://localhost:8080/root File '/home/galaxy/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/controllers/root.py', line 25 in index m_c=m_c, m_a=m_a ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 733 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 744 in fill_template_mako return template.render( **data ) File '/home/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/template.py', line 296 in render return runtime._render(self, self.callable_, args, data) File '/home/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 660 in _render **_kwargs_for_callable(callable_, data)) File '/home/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 691 in _render_context (inherit, lclcontext) = _populate_self_namespace(context, tmpl) File '/home/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 637 in _populate_self_namespace ret = template.module._mako_inherit(template, context) File '/home/galaxy/galaxy-dist/database/compiled_templates/root/index.mako.py', line 25 in _mako_inherit return runtime._inherit_from(context, u'/webapps/galaxy/base_panels.mako', _template_uri) File '/home/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 609 in _inherit_from ret = callable_(template, lclcontext) File '/home/galaxy/galaxy-dist/database/compiled_templates/webapps/galaxy/base_panels.mako.py', line 25 in _mako_inherit return runtime._inherit_from(context, u'/base_panels.mako', _template_uri) File '/home/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 596 in _inherit_from template = _lookup_template(context, uri, calling_uri) File '/home/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 626 in _lookup_template return lookup.get_template(uri) File '/home/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/lookup.py', line 218 in get_template return self._load(srcfile, uri) File '/home/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/lookup.py', line 283 in _load **self.template_args) File '/home/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/template.py', line 218 in __init__ module = self._compile_from_file(path, filename) File '/home/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/template.py', line 245 in _compile_from_file module = imp.load_source(self.module_id, path, open(path, 'rb')) SyntaxError: invalid syntax (base_panels.mako.py, line 301) I have tried replacing the database folder (which is normally on an nfs share) with the original local contents, but no luck. Further I have checked the network share's permissions, but they are all fine. Since Galaxy starts up, ending paster.log with the usual "Serving at 127.0.0.1" I am very puzzled about what's going on. Does anybody has a clue? Thanks. Regards, 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

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Unable to queue job, resubmitting might help
by Geert Vandeweyer 13 Jul '12

13 Jul '12

Hi, Today I ran into a cluster error on our local instance using latest galaxy-dist and torque/pbs with the python-pbs binding. Under heavy load of the galaxy process, it appears that the handler processes failed to contact the pbs-server, although the pbs_server was still up and running. after that, a lot of the following statements kept appearing in the handler.log file: galaxy.jobs.runners.pbs DEBUG 2012-07-11 17:39:06,649 (11647/12788.pbs_master_address) Skipping state check because PBS server connection failed After restarting the galaxy process (run.sh), everything worked again, with no changes to the pbs_server. Would it be possible to setup some checks for this failure? Like: - contact system admin - restart galaxy - auto retry job submission after a while as to not crash workflows. best regards, Geert Vandeweyer -- 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/pub/geert-vandeweyer/26/457/726

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BWA waiting to run
by Thyssen, Gregory - ARS 12 Jul '12

12 Jul '12

Hello, After looking over the posted Q&As, I'd guess that there is simply high volume of NGS data on the public server today, but I'm writing to double-check. My BWA workflows did not run overnight, and show no progress today. I canceled and re-ran the workflows recently, and the BWA is still waiting to run. What should I do? Keep waiting or keep rerunning? Thank you, Gregory Thyssen, PhD Molecular Biologist Cotton Fiber Bioscience USDA-ARS-Southern Regional Research Center 1100 Robert E Lee Blvd New Orleans, LA 70124 gregory.thyssen(a)ars.usda.gov 504-286-4280 This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.

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run_functional_tests.sh issues
by Di Pe 12 Jul '12

12 Jul '12

Hi, I checked out a brand new galaxy-dist to galaxy-runtest I noticed that in order to run it one needs to bootstrap some of the sample files. galaxdev@galaxy1:~/galaxy-runtest$ cp tool_data_table_conf.xml.sample tool_data_table_conf.xml galaxdev@galaxy1:~/galaxy-runtest$ cp datatypes_conf.xml.sample datatypes_conf.xml galaxdev@galaxy1:~/galaxy-runtest$ cp migrated_tools_conf.xml.sample migrated_tools_conf.xml galaxdev@galaxy1:~/galaxy-runtest$ ./run_functional_tests.sh checking how many successes and errors we get : petersen@lamprey:~$ grep -c "Status:</span> success" /home/galaxdev/galaxy-runtest/run_functional_tests.html 138 petersen@lamprey:~$ grep -c "Status:</span> error" /home/galaxdev/galaxy-runtest/run_functional_tests.html 587 the first 20ish tests work but then I am getting the error below. Is this normal? thanks dipe functional.test_get_data.UploadData.test_0010_upload_file Traceback (most recent call last): File "/usr/lib/python2.7/unittest/case.py", line 327, in run testMethod() File "/home/galaxdev/galaxy-runtest/test/functional/test_get_data.py", line 36, in test_0010_upload_file self.upload_file( '4.bed.gz', dbkey='hg17', ftype='bed' ) File "/home/galaxdev/galaxy-runtest/test/base/twilltestcase.py", line 194, in upload_file tc.fv("1","dbkey", dbkey) File "/home/galaxdev/galaxy-runtest/eggs/twill-0.9-py2.7.egg/twill/commands.py", line 450, in formvalue set_form_control_value(control, value) File "/home/galaxdev/galaxy-runtest/eggs/twill-0.9-py2.7.egg/twill/utils.py", line 190, in set_form_control_value raise ClientForm.ItemNotFoundError('cannot find value/label "%s" in list control' % (val,)) ItemNotFoundError: cannot find value/label "hg17" in list control -------------------- >> begin captured stdout << ---------------------

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Galaxy Tool Creation Help
by James Boocock 12 Jul '12

12 Jul '12

Hi All, Just a quick question regarding galaxy tool creation. In the <command> tags Is it possible to get a datasets history number for the history the user initiated the job from? Seems unlikely, the reason I ask is that I have a tool that creates and output file for every input file and the program can take multiple inputs. It would be useful to be able to label the outputs related to the history number so the user could easily identify which output is for which file. Using the multiple output guide something like. primary_${id}_${history dataset number}_visible_txt Cheers James.

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Re: [galaxy-dev] Galaxy tool creation help
by James Boocock 12 Jul '12

12 Jul '12

Hi Guys Regarding my earlier question about history names. I found my answer on the wiki. ${input1.name} was what I was looking for. Cheers James.

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Tophat and bowtie jobs failed!
by A Ghanbarian 11 Jul '12

11 Jul '12

Hi, I have submitted tophat to run on two datasets yesterday morning. The jobs waited in the queue whole yesterday and the statues now show the output files being deleted. Not knowing the architecture that these services are running on, we also tried to submit couple of alignments for smaller datasets which both had the same faith. Now thinking there might be something wrong on the server. My user name is "Avazeh" and tophat jobs are still visible in the history, 52-55 and 60-63. Thanks for all the help, Avazeh

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Job doesn't runnig
by Amandin Talbot 11 Jul '12

11 Jul '12

Dear Galaxy Dev Team- I try to run a job with Tophat for Illumina (version 1.5.0) but in my history job always stay at "Job is waiting to run". I use the following parameters : RNA-Seq FASTQ file: FASTQ Groomer on upload dataset Reference Genome : build-in index : Chicken (Gallus gallus): galGal3 Full Mate-paired : Single-end TopHat settings : Defaults How should i do to make this job running ? Thanks in advance. ________________________ Amandin Talbot

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