galaxy-dev June 2013

galaxy-dev@lists.galaxyproject.org

111 participants
189 discussions

Panels disappearing when choosing tools
by Sebastian Schaaf 19 Jun '13

19 Jun '13

Hi all, Again a question from my side in connection with setting up a new Galaxy instance within an closed network (including a proxy) an SLES 11 SP2. After some struggeling with the Apache config finally Galaxy was accessible, but behaves somewhat strange compared to another instance which is running for a long time without complains (and which was recently updated to the june release). When I choose a tool from the panel on the left side everything works fine until I click on the corresponding link. Unlike the usual case the tools 'GUI' (so the wrapper web page) appears within Galaxy's central pane this side get's 'full screened', means: the panels left (tools), right (history) and on the top side (navigation) are not shown any more. It does not matter wether I'm logged in or not (Galaxy can be accessed by guests currently). Due to the Apache stuff before I compared the access logs of this new instance an the established one: they definitly look different... 'correct': [IP1] - galaxy [19/Jun/2013:19:11:22 +0200] "GET /galaxy/static/style/library.css?v=1370962215 HTTP/1.1" 200 1237 "https://[url]/galaxy/tool_runner?tool_id=upload1" "Mozilla/5.0 (X11; Linux i686) AppleWebKit/537.4 (KHTML, like Gecko) Ubuntu/12.10 Chromium/22.0.1229.94 Chrome/22.0.1229.94 Safari/537.4" 'somewhat strange': [IP2] - - [19/Jun/2013:19:23:16 +0200] "GET /galaxy/tool_runner?tool_id=upload1 HTTP/1.1" 200 35869 Access was performed from the same maschine, using the same browser. What I see is that on the one hand the second field which follows the IP (removed here) is filled with 'galaxy' in the first case, but empty ('-') in the second one. On the other hand it is obvious that most of the info around e.g the accessing browser etc. is missing. The error log does not note anything during this access. Due to the fact that I'm nearly right the opposite of a webserver god (but willed to learn) I would really appreciate your help to fix this. Thanks in advance, Sebastian -- Sebastian Schaaf, M.Sc. Bioinformatics University of Munich

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displaying further input based on previous input
by vijayalakshmi 19 Jun '13

19 Jun '13

Hi all, I am trying to format the input to a java tool that I am writing. I want to display different options to choose from based on the user input. I am not sure how to do that. For example, based on the input file, I want to display the chromosome options to choose from. How do I do this? <param name="input_bam_file" type="data" format="BAM" label="Input BAM file" help="Choose an input BAM file"/> <param name="chromosome_options" type="select" label="Choose the chromosome"> <option value="1"> chr1 </option> <option value="2"> chr2 </option> </param> I am not sure how to call a program that will generate the second input based on the first one and then wait for the user to choose the rest of the input and then run another program. Thanks, VJ.

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Startup error, Galaxy DB got corrupted?
by Leon Mei 19 Jun '13

19 Jun '13

Dear list, Yesterday, I noticed that the user quota setting on our Galaxy had a problem - the list of user email address is missing from the manage quota page. So I thought to give a Galaxy codebase update a try after backing up the Galaxy dir and the database. Running hg head gives me: == postgres@ubuntu:/mnt/galaxyTools/galaxy-2013-05-13$ hg head changeset: 10003:b4a373d86c51 tag: tip parent: 10001:471484ff8be6 user: greg date: Wed Jun 12 11:48:09 2013 -0400 summary: Add targets to Repository Actions menu items. == I updated the DB schema to support the code update. But the restart of Galaxy failed with an error in paster.log: == Traceback (most recent call last): File "/mnt/galaxyTools/galaxy-2013-05-13/lib/galaxy/webapps/galaxy/buildapp.py", line 35, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/mnt/galaxyTools/galaxy-2013-05-13/lib/galaxy/app.py", line 164, in __init__ self.job_manager = manager.JobManager( self ) File "/mnt/galaxyTools/galaxy-2013-05-13/lib/galaxy/jobs/manager.py", line 36, in __init__ self.job_handler.start() File "/mnt/galaxyTools/galaxy-2013-05-13/lib/galaxy/jobs/handler.py", line 34, in start self.job_queue.start() File "/mnt/galaxyTools/galaxy-2013-05-13/lib/galaxy/jobs/handler.py", line 77, in start self.__check_jobs_at_startup() File "/mnt/galaxyTools/galaxy-2013-05-13/lib/galaxy/jobs/handler.py", line 125, in __check_jobs_at_startup self.dispatcher.recover( job, job_wrapper ) File "/mnt/galaxyTools/galaxy-2013-05-13/lib/galaxy/jobs/handler.py", line 620, in recover self.job_runners[runner_name].recover( job, job_wrapper ) File "/mnt/galaxyTools/galaxy-2013-05-13/lib/galaxy/jobs/runners/local.py", line 128, in recover job_wrapper.change_state( model.Job.states.ERROR, info = "This job was killed when Galaxy was restarted. Please retry the job." ) File "/mnt/galaxyTools/galaxy-2013-05-13/lib/galaxy/jobs/__init__.py", line 824, in change_state dataset.state = state File "/mnt/galaxyTools/galaxy-2013-05-13/lib/galaxy/model/__init__.py", line 1163, in set_dataset_state object_session( self ).flush() #flush here, because hda.flush() won't flush the Dataset object File "/mnt/galaxyTools/galaxy-2013-05-13/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 1718, in flush self._flush(objects) File "/mnt/galaxyTools/galaxy-2013-05-13/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 1789, in _flush flush_context.execute() File "/mnt/galaxyTools/galaxy-2013-05-13/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/unitofwork.py", line 331, in execute rec.execute(self) File "/mnt/galaxyTools/galaxy-2013-05-13/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/unitofwork.py", line 475, in execute uow File "/mnt/galaxyTools/galaxy-2013-05-13/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/persistence.py", line 59, in save_obj mapper, table, update) File "/mnt/galaxyTools/galaxy-2013-05-13/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/persistence.py", line 485, in _emit_update_statements execute(statement, params) File "/mnt/galaxyTools/galaxy-2013-05-13/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1449, in execute params) File "/mnt/galaxyTools/galaxy-2013-05-13/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1584, in _execute_clauseelement compiled_sql, distilled_params File "/mnt/galaxyTools/galaxy-2013-05-13/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1698, in _execute_context context) File "/mnt/galaxyTools/galaxy-2013-05-13/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1691, in _execute_context context) File "/mnt/galaxyTools/galaxy-2013-05-13/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.py", line 331, in do_execute cursor.execute(statement, parameters) InternalError: (InternalError) could not read block 326 in file "base/257536/259291": read only 0 of 8192 bytes 'UPDATE dataset SET update_time=%(update_time)s, state=%(state)s WHERE dataset.id = %(dataset_id)s' {'update_time': datetime.datetime(2013, 6, 17, 12, 42, 38, 145908), 'state': 'error', 'dataset_id': 68792} == I went on to check the Galaxy database (in postgres) which confirmed the error in the paster.log. == galaxy=# select * from dataset where id = 68792; id | create_time | update_time | state | deleted | purged | purgable | external_filename | _extra_files_path | file_size | total_size | object_store_id | uuid -------+----------------------------+----------------------------+-------+---------+--------+----------+-------------------+-------------------+-----------+------------+-----------------+------ 68792 | 2013-06-12 06:55:17.608725 | 2013-06-12 06:55:19.396557 | error | f | f | t | | | | | | (1 row) galaxy=# UPDATE dataset SET update_time='2013-06-17 12:42:38.145908', state='error' WHERE dataset.id = 68792; ERROR: could not read block 326 in file "base/257536/259291": read only 0 of 8192 bytes galaxy=# UPDATE dataset SET state='error' WHERE dataset.id = 68792; UPDATE 1 == When I tried to restore the database from the dumped copy I made yesterday, I got the following error: == ERROR: insert or update on table "galaxy_session_to_history" violates foreign key constraint "galaxy_session_to_history_ session_id_fkey" DETAIL: Key (session_id)=(956338) is not present in table "galaxy_session". ERROR: insert or update on table "job" violates foreign key constraint "job_session_id_fkey" DETAIL: Key (session_id)=(852060) is not present in table "galaxy_session". ERROR: insert or update on table "workflow_step_connection" violates foreign key constraint "workflow_step_connection_input_step_id_fkey" DETAIL: Key (input_step_id)=(18422) is not present in table "workflow_step". ERROR: insert or update on table "workflow_step_connection" violates foreign key constraint "workflow_step_connection_output_step_id_fkey" DETAIL: Key (output_step_id)=(18422) is not present in table "workflow_step". == It seems our postgres DB got corrupted? Any suggestion on a fix? Thanks a lot! Leon -- Hailiang (Leon) Mei Netherlands Bioinformatics Center BioAssist NGS Taskforce - http://ngs.nbic.nl<https://wiki.nbic.nl/index.php/Next_Generation_Sequencing> Skype: leon_mei Mobile: +31 6 41709231

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ProFTPD integration with Galaxy
by Malcolm Tobias 18 Jun '13

18 Jun '13

All, I'm attempting to configure ProFTPD to authenticate against the Galaxy database. I appear to be able to connect to the database, but can't authenticate a registered user via FTP. Here are the relevant entries for the ProFTPD configuration: [root@login002 proftpd-1.3.4d]# grep SQL etc/proftpd.conf SQLPasswordEngine on SQLPasswordEncoding hex SQLEngine on SQLBackend postgres SQLConnectInfo galaxydb galaxyftp galaxyftp_password SQLAuthTypes SHA1 SQLAuthenticate users SQLDefaultHomedir /var/opt/local/proftpd SQLLogFile /home/galaxy/proftpd-1.3.4d/var/sql.log SQLUserInfo custom:/LookupGalaxyUser SQLNamedQuery LookupGalaxyUser SELECT "email,password,'4630','1108','/home/galaxy/galaxy-dist/database/files/ftp/%U','/bin/bash' FROM galaxy_user WHERE email='%U'" I'm starting the daemon with maximum verbosity: [root@login002 proftpd-1.3.4d]# ./sbin/proftpd -n -d 10 The logs appear to be OK: Jun 18 12:37:09 mod_sql/4.3[987]: defaulting to 'postgres' backend Jun 18 12:37:09 mod_sql/4.3[987]: backend module 'mod_sql_postgres/4.0.4' Jun 18 12:37:09 mod_sql/4.3[987]: backend api 'mod_sql_api_v1' Jun 18 12:37:09 mod_sql/4.3[987]: >>> sql_sess_init Jun 18 12:37:09 mod_sql/4.3[987]: entering postgres cmd_defineconnection Jun 18 12:37:09 mod_sql/4.3[987]: name: 'default' Jun 18 12:37:09 mod_sql/4.3[987]: user: 'galaxyftp' Jun 18 12:37:09 mod_sql/4.3[987]: host: 'localhost' Jun 18 12:37:09 mod_sql/4.3[987]: db: 'galaxydb' Jun 18 12:37:09 mod_sql/4.3[987]: port: '5432' Jun 18 12:37:09 mod_sql/4.3[987]: ttl: '0' Jun 18 12:37:09 mod_sql/4.3[987]: exiting postgres cmd_defineconnection Jun 18 12:37:09 mod_sql/4.3[987]: connection 'default' successfully established Jun 18 12:37:09 mod_sql/4.3[987]: mod_sql engine : on Jun 18 12:37:09 mod_sql/4.3[987]: negative_cache : off Jun 18 12:37:09 mod_sql/4.3[987]: authenticate : users Jun 18 12:37:09 mod_sql/4.3[987]: usertable : users Jun 18 12:37:09 mod_sql/4.3[987]: userid field : userid Jun 18 12:37:09 mod_sql/4.3[987]: password field : passwd Jun 18 12:37:09 mod_sql/4.3[987]: UID field : uid Jun 18 12:37:09 mod_sql/4.3[987]: GID field : gid Jun 18 12:37:09 mod_sql/4.3[987]: homedir field : homedir Jun 18 12:37:09 mod_sql/4.3[987]: homedir(default) : '/var/opt/local/proftpd' Jun 18 12:37:09 mod_sql/4.3[987]: shell field : shell Jun 18 12:37:09 mod_sql/4.3[987]: SQLMinUserUID : 999 Jun 18 12:37:09 mod_sql/4.3[987]: SQLMinUserGID : 999 Jun 18 12:37:09 mod_sql/4.3[987]: <<< sql_sess_init Jun 18 12:37:15 mod_sql/4.3[987]: >>> sql_pre_pass Jun 18 12:37:15 mod_sql/4.3[987]: <<< sql_pre_pass Jun 18 12:37:15 mod_sql/4.3[987]: >>> cmd_getpwnam Jun 18 12:37:15 mod_sql/4.3[987]: entering postgres cmd_escapestring Jun 18 12:37:15 mod_sql/4.3[987]: entering postgres cmd_open Jun 18 12:37:15 mod_sql/4.3[987]: Postgres server version: 8.1.23 Jun 18 12:37:15 mod_sql/4.3[987]: connection 'default' opened Jun 18 12:37:15 mod_sql/4.3[987]: connection 'default' count is now 2 Jun 18 12:37:15 mod_sql/4.3[987]: exiting postgres cmd_open Jun 18 12:37:15 mod_sql/4.3[987]: entering postgres cmd_close Jun 18 12:37:15 mod_sql/4.3[987]: connection 'default' count is now 1 Jun 18 12:37:15 mod_sql/4.3[987]: exiting postgres cmd_close Jun 18 12:37:15 mod_sql/4.3[987]: exiting postgres cmd_escapestring Jun 18 12:37:15 mod_sql/4.3[987]: cache miss for user 'mtobias(a)wustl.edu' Jun 18 12:37:15 mod_sql/4.3[987]: >>> sql_lookup Jun 18 12:37:15 mod_sql/4.3[987]: >>> process_named_query 'LookupGalaxyUser' Jun 18 12:37:15 mod_sql/4.3[987]: entering postgres cmd_escapestring Jun 18 12:37:15 mod_sql/4.3[987]: entering postgres cmd_open Jun 18 12:37:15 mod_sql/4.3[987]: connection 'default' count is now 2 Jun 18 12:37:15 mod_sql/4.3[987]: exiting postgres cmd_open Jun 18 12:37:15 mod_sql/4.3[987]: entering postgres cmd_close Jun 18 12:37:15 mod_sql/4.3[987]: connection 'default' count is now 1 Jun 18 12:37:15 mod_sql/4.3[987]: exiting postgres cmd_close Jun 18 12:37:15 mod_sql/4.3[987]: exiting postgres cmd_escapestring Jun 18 12:37:15 mod_sql/4.3[987]: entering postgres cmd_escapestring Jun 18 12:37:15 mod_sql/4.3[987]: entering postgres cmd_open Jun 18 12:37:15 mod_sql/4.3[987]: connection 'default' count is now 2 Jun 18 12:37:15 mod_sql/4.3[987]: exiting postgres cmd_open Jun 18 12:37:15 mod_sql/4.3[987]: entering postgres cmd_close Jun 18 12:37:15 mod_sql/4.3[987]: connection 'default' count is now 1 Jun 18 12:37:15 mod_sql/4.3[987]: exiting postgres cmd_close Jun 18 12:37:15 mod_sql/4.3[987]: exiting postgres cmd_escapestring Jun 18 12:37:15 mod_sql/4.3[987]: entering postgres cmd_select Jun 18 12:37:15 mod_sql/4.3[987]: entering postgres cmd_open Jun 18 12:37:15 mod_sql/4.3[987]: connection 'default' count is now 2 Jun 18 12:37:15 mod_sql/4.3[987]: exiting postgres cmd_open Jun 18 12:37:15 mod_sql/4.3[987]: query "SELECT email,password,'4630','1108','/home/galaxy/galaxy-dist/database/files/ftp/mtobias(a)wustl.edu','/bin/bash' FROM galaxy_user WHERE email='mtobias(a)wustl.edu'" Jun 18 12:37:15 mod_sql/4.3[987]: entering postgres cmd_close Jun 18 12:37:15 mod_sql/4.3[987]: connection 'default' count is now 1 Jun 18 12:37:15 mod_sql/4.3[987]: exiting postgres cmd_close Jun 18 12:37:15 mod_sql/4.3[987]: exiting postgres cmd_select Jun 18 12:37:15 mod_sql/4.3[987]: <<< process_named_query 'LookupGalaxyUser' Jun 18 12:37:15 mod_sql/4.3[987]: <<< sql_lookup Jun 18 12:37:15 mod_sql/4.3[987]: cache miss for user 'mtobias(a)wustl.edu' Jun 18 12:37:15 mod_sql/4.3[987]: user 'mtobias(a)wustl.edu' cached Jun 18 12:37:15 mod_sql/4.3[987]: + pwd.pw_name : mtobias(a)wustl.edu Jun 18 12:37:15 mod_sql/4.3[987]: + pwd.pw_uid : 4630 Jun 18 12:37:15 mod_sql/4.3[987]: + pwd.pw_gid : 1108 Jun 18 12:37:15 mod_sql/4.3[987]: + pwd.pw_dir : /home/galaxy/galaxy-dist/database/files/ftp/mtobias(a)wustl.edu Jun 18 12:37:15 mod_sql/4.3[987]: + pwd.pw_shell : /bin/bash Jun 18 12:37:15 mod_sql/4.3[987]: <<< cmd_getpwnam Jun 18 12:37:15 mod_sql/4.3[987]: >>> cmd_auth Jun 18 12:37:15 mod_sql/4.3[987]: entering postgres cmd_escapestring Jun 18 12:37:15 mod_sql/4.3[987]: entering postgres cmd_open Jun 18 12:37:15 mod_sql/4.3[987]: connection 'default' count is now 2 Jun 18 12:37:15 mod_sql/4.3[987]: exiting postgres cmd_open Jun 18 12:37:15 mod_sql/4.3[987]: entering postgres cmd_close Jun 18 12:37:15 mod_sql/4.3[987]: connection 'default' count is now 1 Jun 18 12:37:15 mod_sql/4.3[987]: exiting postgres cmd_close Jun 18 12:37:15 mod_sql/4.3[987]: exiting postgres cmd_escapestring Jun 18 12:37:15 mod_sql/4.3[987]: cache hit for user 'mtobias(a)wustl.edu' Jun 18 12:37:15 mod_sql/4.3[987]: >>> cmd_check Jun 18 12:37:15 mod_sql/4.3[987]: checking password using SQLAuthType 'sha1' Jun 18 12:37:15 mod_sql/4.3[987]: 'sha1' SQLAuthType handler reports failure Jun 18 12:37:15 mod_sql/4.3[987]: <<< cmd_check Jun 18 12:37:15 mod_sql/4.3[987]: <<< cmd_auth At the same time, I'm seeing from the command line: login002 proftpd[987] login002 (10.28.56.101[10.28.56.101]): mod_sql_passwd/0.4: expected 'PBKDF2$sha256$10000$8h/4HmD1Eu6NTc7F$Slb1H5a9YJvR6A3cUnZCUfh7tOWKfRuh', got 'cc0ef515d684386aaa500bf6499d9f512dfb332c' It almost looks like it's expecting a longer string, maybe with a salt and I'm not sure why it's expecting SHA256 as I thought all of Galaxy was using SHA1? I tried changing SQLAuthTypes to SHA256 without luck. Any suggestions on what to look at to debug this further? Thanks, Malcolm -- Malcolm Tobias 314.362.1594

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Cannot configure DRMAA
by Patel, Viren 18 Jun '13

18 Jun '13

Hello. I have installed Galaxy and run it successfully. Now I am trying to configure it to use DRMAA job runner. I created a job_conf.xml file as explained in the Galaxy wiki: <?xml version="1.0"?> <job_conf> <plugins> <plugin id="sge" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner" workers="4"/> </plugins> <destinations default="sge_default"> <destination id="sge_default" runner="drmaa"/> </destinations> </job_conf> The galaxy user has the necessary environment variable: $ echo $DRMAA_LIBRARY_PATH /opt/sge/lib/lx-amd64/libdrmaa.so But then Galaxy does not start. Here are the final log messages: galaxy.jobs DEBUG 2013-06-17 17:32:27,715 Loading job configuration from ./job_conf.xml Traceback (most recent call last): File "/mnt/FSS2/data/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 35, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/mnt/FSS2/data/home/galaxy/galaxy-dist/lib/galaxy/app.py", line 97, in __init__ self.job_config = jobs.JobConfiguration(self) File "/mnt/FSS2/data/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 109, in __init__ self.__parse_job_conf_xml(tree) File "/mnt/FSS2/data/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 159, in __parse_job_conf_xml self.default_handler_id = self.__get_default(handlers, self.handlers.keys()) File "/mnt/FSS2/data/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 288, in __get_default rval = parent.get('default') AttributeError: 'NoneType' object has no attribute 'get' Removing PID file galaxy-web1.pid I am using the following to start Galaxy: /bin/sh run.sh --pid-file galaxy.pid --log-file galaxy.log I have updated my Galaxy install to the latest stable version, but the problem persists. Any help will be much appreciated. Please note that Galaxy runs ok without the job_conf.xml file. Is there some configuration I am missing? Thanks. Viren ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

2 1

Best practices for a local install of Galaxy
by Paul St. Amand 18 Jun '13

18 Jun '13

On Jun 18, 2013, at 8:02 AM, galaxy-dev-request(a)lists.bx.psu.edu wrote: > I have Galaxy running on a small Mac workstation. I have made a specific > user, 'galaxy', for it. It is cleaner, but probably overkill for 1 person. > > Note also that you can install a daemon to start Galaxy automatically > when your computer starts: > https://bitbucket.org/galaxy/galaxy-central/src/d2d4b6ac2139f1623301990462a… > > I don't think I have ever waited long enough to see the end of the unit > tests. If some fail without any obvious reason (missing dependencies or > what not), you should probably raise this issue on the Galaxy mailing > list or bug tracker. > > Cheers, > > Florent Thanks for the startup tip Florent. That would be useful for those using Galaxy daily. So you think that running the install as the current non-root but ADMIN user works OK? What about the install folder? Must it be the home folder or is a subfolder OK as I have it (/Users/pst/Applications/)? My test output "run_functional_tests.html" is 5.1MB. I suppose that is too much to post on the list. I think that most of the errors are not due to dependencies. How do I get help with that? Paul

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Trying to configure external data source
by Daniel Gorelik 18 Jun '13

18 Jun '13

Hello folks, I am trying to configure an external data source and it is driving me crazy. I keep getting the error "The remote data source application has not sent back a URL parameter in the request." , even though it is. My xml file is: <?xml version="1.0"?> <tool name="My tool" id="s3t" tool_type="data_source"> <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> <inputs action="myurl/" check_values="true" method="get"> <display>Let's do this! $GALAXY_URL</display> <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=s3t" /> <param name="sendToGalaxy" type="hidden" value="1"/> </inputs> <request_param_translation> <request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" /> <request_param galaxy_name="URL" remote_name="URL" missing="myurl/" /> </request_param_translation> <uihints minwidth="800"/> <outputs> <data name="output" format="txt" label="test" /> </outputs> <options sanitize="False" refresh="True"/> </tool> And in myurl file I have: <FORM ACTION="%s" METHOD=POST> <input type="submit"></input> <INPUT TYPE=HIDDEN NAME='URL' VALUE='myfile/'> </form> %s is the GALAXY_URL Any help, pointers, or philosophical advice would be greatly appreciated. Thank you, Daniel Gorelik

1 0

setting parameters for uploading a file for a java program
by vijayalakshmi 18 Jun '13

18 Jun '13

Hi all, I have a tool written in java for which I want to upload a file as a parameter. I have trouble figuring out how to do it. I tried writing the xml file similar to 'tools/data-source/upload.xml' but it is not working. *correlation.xml* <tool id="correlation" name="Compute correlation" version="1.1.3"> <description> for the given BAM file </description> <action module="galaxy.tools.actions.upload" class="UploadToolAction"/> <command>java -jar Correlation.jar $input_bam_file $output</command> <inputs nginx_upload="true"> <param name="async_datasets" type="hidden" value="None"/> <upload_dataset name="input" title="Specify Files for Dataset" file_type_name="file_type" metadata_ref="files_metadata"> <param name="input_bam_file" type="file" size="30" label="File (Please avoid Windows format text file)" ajax-upload="true" help="TIP1: Due to browser limitations"> <validator type="expression" message="You will need to reselect the file you specified (%s)." substitute_value_in_message="True">not ( ( isinstance( value, unicode ) or isinstance( value, str ) ) and value != "" )</validator> </param> </upload_dataset> <param name="dbkey" type="genomebuild" label="Genome" /> <conditional name="files_metadata" title="Specify metadata" value_from="self:app.datatypes_registry.get_upload_metadata_params" value_ref="file_type" value_ref_in_group="False" /> </inputs> <outputs> <data name="output" format="txt" /> </outputs> </tool> I am not sure where I am making a mistake... Is the procedure to upload a file for java different from python? Thanks, VJ.

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Clone Galaxy from repository: mercurial from behind proxy?
by Sebastian Schaaf 18 Jun '13

18 Jun '13

Hi all, I'm currently trying to set up a galaxy-dist instance on a SLES server within an 'encapsulated' network (hospital environment; here all sensitive data is stored and handled). Within this network, clients are only capable of accessing the internet via HTTP/HTTPS and FTP, using a proxy - adress and port (8080) are the same for all three protocols. Mercurial (which I had to set up in advance) is accessible and more or less in default configuration (more on that down below). What I get after executing the command 'hg clone https://bitbucket.org/galaxy/galaxy-dist#stable' is "abort: error: _ssl.c:491: error:140700FC:SSL routines:SSL23_GET_SERVER_HELLO:unknown protocol" Google search indicates something more general, so outside the exclusive scope of Galaxy. On top, no connection to Galaxy was listed, also not in this mailing list's archive. Following some hints I just tried to set the proxy via a '.hgrc' file in the galaxy user home like this: --- [http_proxy] host = url:port [https_proxy] host = url:port --- (re-login after that) and also set the system variables '$http_proxy' and '$https_proxy'. Another approach described was to call 'hg --config http_proxy.host=url:port clone https://bitbucket.org/galaxy/galaxy-dist#stable' Nothing worked out. Does anyone experienced similar behaviour or has got some ideas how to solve this? Thanks in advance, Sebastian -- Sebastian Schaaf, M.Sc. Bioinformatics University of Munich

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Galaxy setup from cloudman shows no tools in the tool panel
by Marco Ocana 18 Jun '13

18 Jun '13

Hi, Just setup Galaxy using cloudman on AWS. I updated the version of Galaxy using the Admin Console (it shows revision 10066:d2d4b6ac2139<http://bitbucket.org/galaxy/galaxy-central/changesets/d2d4b6ac2139> ). I also did the additional tool installation described in the Galaxy log file by running the script: sh ./scripts/migrate_tools/0007_tools.sh install_dependencies FInally, I added the genomespace tools as described in: http://wiki.galaxyproject.org/GenomeSpace >From the cloudman admin console all systems appear as "Running" . However, when I go to the Galaxy main page, the "Tools" panel is completely empty. I tried restarting Galaxy from the cloudman console a couple of times. There are errors that show up in the Galaxy log, though none that could tell me precisely what I should do to get the tools to display. I have attached the Galaxy log file. Any help would be appreciated. Thanks Marco

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galaxy-dev June 2013