- galaxy-dev - lists.galaxyproject.org

Regarding galaxy wrappers: "lumi", "DESeq" "edgeR"
by Sachit Adhikari 08 Jul '13

08 Jul '13

Hi, These are the R libraries. Have anyone written a wrapper for these libraries "lumi", "DESeq" "edgeR"? Thanks, Sachit

3 5

Postgresql database not working
by Sajoscha Sauer 08 Jul '13

08 Jul '13

Hi all, I just installed the newest version of Galaxy with: hg clone https://bitbucket.org/galaxy/galaxy-dist I use Apache httpd as proxy and ldap authentication. If I leave the database as it is set by default everything works fine. sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE But if I now change to postgres my histories cannot be fetched. I'm not sure how to explain it, but every time I refresh the history panel a new history is created. The database connection is fine, it also creates the history entries in the database, but something is wrong. Has someone an idea or can help? Thanks a lot! Cheers, Sajoscha

1 1

Question about bowtie2_indeces.loc
by Perez, Ricardo 07 Jul '13

07 Jul '13

Dear all, When adding a genome I understand that the format are added in the following way: <unique_build_id> <dbkey> <display_name> <file_base_path> My question is, what is the difference between the unique_build_id and the dbkey? Thank you for your time, --Ricardo Perez

2 1

instance restart fails with AttributeError: 'module' object has no attribute 'DataManagerHistoryAssociation'
by Vipin TS 06 Jul '13

06 Jul '13

Hello dev-team, I am trying to upgrade our production instance to the latest release (to galaxy-dist) , somehow I am not able to restart the instance. Here is the log message I found: File "./scripts/paster.py", line 35, in <module> serve.run() File "galaxy-prod-repo/lib/galaxy/util/pastescript/serve.py", line 1049, in run invoke(command, command_name, options, args[1:]) File "galaxy-prod-repo/lib/galaxy/util/pastescript/serve.py", line 1055, in invoke exit_code = runner.run(args) File "galaxy-prod-repo/lib/galaxy/util/pastescript/serve.py", line 220, in run result = self.command() File "galaxy-prod-repo/lib/galaxy/util/pastescript/serve.py", line 643, in command app = loadapp( app_spec, name=app_name, relative_to=base, global_conf=vars) File "galaxy-prod-repo/lib/galaxy/util/pastescript/loadwsgi.py", line 350, in loadapp return loadobj(APP, uri, name=name, **kw) File "galaxy-prod-repo/lib/galaxy/util/pastescript/loadwsgi.py", line 374, in loadobj global_conf=global_conf) File "galaxy-prod-repo/lib/galaxy/util/pastescript/loadwsgi.py", line 399, in loadcontext global_conf=global_conf) File "galaxy-prod-repo/lib/galaxy/util/pastescript/loadwsgi.py", line 423, in _loadconfig return loader.get_context(object_type, name, global_conf) File "galaxy-prod-repo/lib/galaxy/util/pastescript/loadwsgi.py", line 561, in get_context section) File "galaxy-prod-repo/lib/galaxy/util/pastescript/loadwsgi.py", line 620, in _context_from_explicit value = import_string(found_expr) File "galaxy-prod-repo/lib/galaxy/util/pastescript/loadwsgi.py", line 125, in import_string return pkg_resources.EntryPoint.parse("x=" + s).load(False) File "galaxy-prod-repo/lib/pkg_resources.py", line 1954, in load entry = __import__(self.module_name, globals(),globals(), ['__name__']) File "galaxy-prod-repo/lib/galaxy/web/buildapp.py", line 3, in <module> from galaxy.webapps.galaxy.buildapp import app_factory File "galaxy-prod-repo/lib/galaxy/webapps/galaxy/buildapp.py", line 18, in <module> import galaxy.model.mapping File "galaxy-prod-repo/lib/galaxy/model/mapping.py", line 943, in <module> Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ) AttributeError: 'module' object has no attribute 'DataManagerHistoryAssociation' Removing PID file paster.pid I am not clear about the error message here. any idea thank you, --/Vipin cBio MSKCC Ratsch Lab

2 1

phastCons scores all NaN
by diana 05 Jul '13

05 Jul '13

Hi all, I am a new user to Galaxy. Recently I uploaded a bed file to Galaxy and then converted it to hg18 format in order to run a phastCons scoring on it. The fields returned were all NaN, though. I then converted the hg18 format to hg17 in order to see if that would make a difference, but it still returned NaN each time. At this point, in order to test if it was simply my data that had a problem, I found and viewed a specific region in the UCSC genome browser to verify that it did, in fact, include regions with conservation, I entered that sequence into Galaxy in bed format and attempted to get phastCons scores for it, but still received NaN for the results. At this point, I have no idea what is going on. I believe that this must be a bug, since I am fairly certain that my bed files are in the correct format. All of these were run on the main Galaxy server on and off during the past week. If anyone could help me figure out what is wrong, I would appreciate it very much. Thanks, Diana

1 0

Scripts interacting with the database
by Lee Katz 05 Jul '13

05 Jul '13

Sorry for being really verbose on this list recently, but we are making a huge push for Galaxy right now. Hopefully you all aren't annoyed by me yet...! One thing we want to do after a MiSeq run is to run all assemblies and then report certain statistics such as N50. These metrics would then be reported in an exportable spreadsheet for our molecular biologists. I have the scripts ready to calculate these metrics. My questions here are: 1) Is there any kind of existing functionality that is close to what I want? 2) If not, 2a) Is there a way to trigger some scripts for assembly and metrics (and maybe more) once a MiSeq dumps all the data into Galaxy? 2b) Is there a certain convention on interaction with the database? And documentation on that? 2c) Is there an existing convention on reading the Galaxy database, so that I can produce the spreadsheet? Documentation? 2d) Our lab would call this functionality Rover, since it will roam Galaxy looking for and retrieving data (not really a question, but I thought they came up with a good name!) -- Lee Katz, Ph.D.

2 1

Startup problem after upgrade
by Bertrand PITOLLAT 04 Jul '13

04 Jul '13

Hi, I have just upgraded my galaxy instance. When trying to access my galaxy instance home page, I get the following error : 195.221.174.40 - - [02/Jul/2013:15:34:23 +0200] "GET / HTTP/1.1" 500 - "-" "Mozilla/5.0 (Windows NT 6.1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/27.0.1453.116 Safari/537.36" Error - <class 'mako.exceptions.TopLevelLookupException'>: Cant locate template for uri 'root/index.mako' URL: http://marmadais.cirad.fr:7090/ File '/SATA/bioinfo/galaxy_dev/galaxy_dist/lib/galaxy/web/framework/middleware/ error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/SATA/bioinfo/galaxy_dev/galaxy_dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/r ecursive.py', line 84 in __call__ return self.application(environ, start_response) File '/SATA/bioinfo/galaxy_dev/galaxy_dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/h ttpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/SATA/bioinfo/galaxy_dev/galaxy_dist/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/SATA/bioinfo/galaxy_dev/galaxy_dist/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/SATA/bioinfo/galaxy_dev/galaxy_dist/lib/galaxy/webapps/galaxy/controller s/root.py', line 39 in index params=kwd ) File '/SATA/bioinfo/galaxy_dev/galaxy_dist/lib/galaxy/web/framework/__init__.py ', line 957 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/SATA/bioinfo/galaxy_dev/galaxy_dist/lib/galaxy/web/framework/__init__.py ', line 964 in fill_template_mako template = self.webapp.mako_template_lookup.get_template( filename ) File '/SATA/bioinfo/galaxy_dev/galaxy_dist/eggs/Mako-0.4.1-py2.6.egg/mako/looku p.py', line 221 in get_template "Cant locate template for uri %r" % uri) TopLevelLookupException: Cant locate template for uri 'root/index.mako' Any help welcome. Bertrand.

2 3

Empty & 'no peek' Returned Instead of HTML Output?
by Amanda Zuzolo 04 Jul '13

04 Jul '13

I recently updated my local testing Galaxy install to the latest stable version. When I went to test the working of HTML output in some scripts that worked in previous installs of Galaxy, the latest stable version gave me an empty return with a message of 'no peek' rather than outputting the HTML file with the embedded Javascript functionality. Additionally, the HTML output from previous runs of the same tool no longer shows the Javascript file/functionality when opened from the eye button in Galaxy, but still works fine from the HTML file opened out of the file directory. Any assistance on this issue would be greatly appreciated. -- Amanda Zuzolo Bioengineering Major, George Mason University Metabiome Informatics Group, Environmental Biocomplexity

2 1

sqlite to postgresql conversion
by Lee Katz 03 Jul '13

03 Jul '13

Hi, I am realizing, hopefully not to late, that I need to convert my database to postgresql so that I can have concurrent sessions and all the other goodness that it brings to the table. Is there an easy way to convert? I am trying to do it on the command line, but it isn't working so well. I am kind of new to postgres and even sqlite I tried this dump/import command, but it does not work. It didn't seem to like "PRAGMA" so I removed it (sqlite3 universe.sqlite .dump|grep -v 'PRAGMA'|psql chapman galaxy) 2>&1|less BEGIN NOTICE: CREATE TABLE / PRIMARY KEY will create implicit index "migrate_version_pkey" for table "migrate_version" CREATE TABLE INSERT 0 1 NOTICE: CREATE TABLE / PRIMARY KEY will create implicit index "dataset_pkey" for table "dataset" CREATE TABLE ERROR: column "deleted" is of type boolean but expression is of type integer LINE 1: ...5:50:25.714594','2013-06-28 15:51:00.760008','ok',0,0,0,'/me... ^ HINT: You will need to rewrite or cast the expression. ERROR: current transaction is aborted, commands ignored until end of transaction block ERROR: current transaction is aborted, commands ignored until end of transaction block ERROR: current transaction is aborted, commands ignored until end of transaction block

1 1

samtools BAM to SAM tmp directory
by Matt Shirley 03 Jul '13

03 Jul '13

Is there a reason that the samtools BAM to SAM does not respect the new_file_path set in the config file? The tmp directory handling by different tool wrappers seems to be an issue right now on systems with small system tmp directories. -- Matt Shirley Ph.D Candidate - BCMB Pevsner Lab <http://pevsnerlab.kennedykrieger.org/> Johns Hopkins Medicine

3 4