[galaxy-dev] datatype directory
Why isn't there a datatype for a directory of files? This seems like such a simple thing. If an executable generates or expects a directory as its input or output, why must a fancy complicated composite datatype be created to handle this? David Hoover David Hoover, PhD Helix Systems Staff SCB/DCSS/CIT/NIH 301-435-2986 http://helix.nih.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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] tool for STAR RNA-seq aligner
A colleague of mine mentioned it. I'll ask him where he got his info. Just to clarify: do you always run STAR jobs on the same host? We are running Galaxy in front of a batch system cluster, and so by default STAR jobs would run on different nodes. It's not clear to me how long the memory allocated would last after the batch job finished. How do you determine whether the memory remains allocated and whether the job has been accelerated due to pre-loaded data? For example, if you create a genome reference, using --genomeLoad=LoadAndKeep, then run an alignment, are subsequent alignments using the same genome reference much faster? If so, how much faster? I apologize, I am a jack of all trades, master of none. I could test this myself, but everything I touch related to genomics takes 50GB of memory and 18 hours clocktime, and it gets painful to try testing everything. David David Hoover, PhD Helix Systems Staff SCB/DCSS/CIT/NIH 301-435-2986 http://helix.nih.gov On Sep 26, 2014, at 4:13 AM, Ross ross.laza...@gmail.com wrote: Hi David. I've not needed that workflow so haven't a solution for you and no, it doesn't do anything with chimeric output - won't be hard to add I suspect. There's no python wrapper - just shell script in the command segment. It's not in an IUC main tool shed repository because it lacks a data manager - manual star indexes are a bit of a pain but less pain than writing a data manager :( so I haven't yet. Might be run best through the API. On shared memory: Pity. it works a treat for us. I didn't see anything on the google group - do you recall where you learned about this deprecation ? On Thu, Sep 25, 2014 at 10:41 PM, David Hoover hoove...@helix.nih.gov wrote: Ross, About the index files: It is way easier to have pre-built index files. However, when running a 2-pass STAR run, a user will need to generate their own reference index files based on the output SJ.tab.out file created in the first pass. Is this incorporated into your tool? About shared memory: I am under the impression that the latest version of STAR has deprecated this feature. I am unclear how this would help unless a single large-memory machine was dedicated to running all STAR jobs. Is this the case? Also, does the tool merge the SAM/BAM file with the output chimeric SAM file? David Hoover On 9/24/2014 7:03 PM, Ross wrote: Hi All, That (fubar in testtoolshed) star wrapper was derived from one originally written by Jeremy Goecks. I modified it for multiple inputs and added a few tweaks and it has been in production use in our group for about 6 months so I'm pretty sure it works reasonably well in our hands at least. I would really appreciate any available help getting it to a proven useful state - suggestions and code welcomed. I have not moved it to the main toolshed because aside from some encouragement, I've had no feedback to suggest it's working - or not. It is extremely fast - we regularly see 200-300M reads per minute in the logs! We regularly run a whole experiment worth (eg 12 - 24) fastq files simultaneously with the shared memory option working on our cluster - see the readme. Star index files made with a gene model (requires valid gff3) are huge - 20-30GB for hg19 - hence the need for shared memory if you run multiple jobs. That will eventually become a serious problem if you really want to allow users to make their own - we definitely do not. You need to be very careful about matching the gene model gff3 file to the reference and I had enough trouble getting it right for the few major genomes we use to make me think that I do not want users trying to do that generating 25GB of rubbish every time they get it wrong. There are challenges to do with needing different indexes for different length reads but we are seeing fairly consistent 60bp single ended reads for most of the incoming RNA seq experiments. A data manager would be a boon if anyone cares to write one... On Thu, Sep 25, 2014 at 6:55 AM, Curtis Hendrickson (Campus) curt...@uab.edu wrote: Bjorn We'd be interested in this tool, as well. Any idea how close to functional it is? I see it's only on TEST toolshed, and not on production, at this point. I don't see any related Trello card when searching on star Regards, Curtis Galaxy Admin @ University of Alabama at Birmingham -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Björn Grüning Sent: Wednesday, September 24, 2014 3:15 PM To: galaxy-dev@lists.bx.psu.edu; hoove...@helix.nih.gov David Hoover Subject: Re: [galaxy-dev] tool for STAR RNA-seq aligner Hi David, yes there is inital code in the https://testtoolshed.g2.bx.psu.edu/. I think Ross has done some work on it. The main problem with Star is that is needs special indices
Re: [galaxy-dev] tool for STAR RNA-seq aligner
Ross, About the index files: It is way easier to have pre-built index files. However, when running a 2-pass STAR run, a user will need to generate their own reference index files based on the output SJ.tab.out file created in the first pass. Is this incorporated into your tool? About shared memory: I am under the impression that the latest version of STAR has deprecated this feature. I am unclear how this would help unless a single large-memory machine was dedicated to running all STAR jobs. Is this the case? Also, does the tool merge the SAM/BAM file with the output chimeric SAM file? David Hoover On 9/24/2014 7:03 PM, Ross wrote: Hi All, That (fubar in testtoolshed) star wrapper was derived from one originally written by Jeremy Goecks. I modified it for multiple inputs and added a few tweaks and it has been in production use in our group for about 6 months so I'm pretty sure it works reasonably well in our hands at least. I would really appreciate any available help getting it to a proven useful state - suggestions and code welcomed. I have not moved it to the main toolshed because aside from some encouragement, I've had no feedback to suggest it's working - or not. It is extremely fast - we regularly see 200-300M reads per minute in the logs! We regularly run a whole experiment worth (eg 12 - 24) fastq files simultaneously with the shared memory option working on our cluster - see the readme. Star index files made with a gene model (requires valid gff3) are huge - 20-30GB for hg19 - hence the need for shared memory if you run multiple jobs. That will eventually become a serious problem if you really want to allow users to make their own - we definitely do not. You need to be very careful about matching the gene model gff3 file to the reference and I had enough trouble getting it right for the few major genomes we use to make me think that I do not want users trying to do that generating 25GB of rubbish every time they get it wrong. There are challenges to do with needing different indexes for different length reads but we are seeing fairly consistent 60bp single ended reads for most of the incoming RNA seq experiments. A data manager would be a boon if anyone cares to write one... On Thu, Sep 25, 2014 at 6:55 AM, Curtis Hendrickson (Campus) curt...@uab.edu mailto:curt...@uab.edu wrote: Bjorn We'd be interested in this tool, as well. Any idea how close to functional it is? I see it's only on TEST toolshed, and not on production, at this point. I don't see any related Trello card when searching on star Regards, Curtis Galaxy Admin @ University of Alabama at Birmingham -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edu mailto:galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Björn Grüning Sent: Wednesday, September 24, 2014 3:15 PM To: galaxy-dev@lists.bx.psu.edu mailto:galaxy-dev@lists.bx.psu.edu; hoove...@helix.nih.gov mailto:hoove...@helix.nih.gov David Hoover Subject: Re: [galaxy-dev] tool for STAR RNA-seq aligner Hi David, yes there is inital code in the https://testtoolshed.g2.bx.psu.edu/. I think Ross has done some work on it. The main problem with Star is that is needs special indices (and a lot of it) and it would be great to offer data managers for it. Cheers, Bjoern Am 24.09.2014 um 22:05 schrieb David Hoover: Hi, I am developing a tool for STAR (https://code.google.com/p/rna-star/), and I realize I may be reinventing another wheel. Has anyone else created a tool for STAR? There's nothing else in the toolsheds for it yet. David David Hoover, PhD Helix Systems Staff SCB/DCSS/CIT/NIH 301-435-2986 http://helix.nih.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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy
[galaxy-dev] tool for STAR RNA-seq aligner
Hi, I am developing a tool for STAR (https://code.google.com/p/rna-star/), and I realize I may be reinventing another wheel. Has anyone else created a tool for STAR? There's nothing else in the toolsheds for it yet. David David Hoover, PhD Helix Systems Staff SCB/DCSS/CIT/NIH 301-435-2986 http://helix.nih.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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] tool for STAR RNA-seq aligner
Why didn't I see these before? Hmm, I thought I had searched both toolsheds... I was kind of hoping someone had tackled this in a different way. It would be nice if there was a composite datatype for the reference genome. It is important for users to generate their own personal genome references, rather than rely on shared, admin-installed indices. And you're correct, we'd need at least 5-10 separate genome references for each organism, depending on read length and annotation GTF. Back to wheel reinvention. BTW, can you tell me which standardly installed tools use composite datatypes? It's always easier to build thing from comparison, rather than from scratch. David David Hoover, PhD Helix Systems Staff On Sep 24, 2014, at 4:14 PM, Björn Grüning bjoern.gruen...@gmail.com wrote: Hi David, yes there is inital code in the https://testtoolshed.g2.bx.psu.edu/. I think Ross has done some work on it. The main problem with Star is that is needs special indices (and a lot of it) and it would be great to offer data managers for it. Cheers, Bjoern Am 24.09.2014 um 22:05 schrieb David Hoover: Hi, I am developing a tool for STAR (https://code.google.com/p/rna-star/), and I realize I may be reinventing another wheel. Has anyone else created a tool for STAR? There's nothing else in the toolsheds for it yet. David David Hoover, PhD Helix Systems Staff SCB/DCSS/CIT/NIH 301-435-2986 http://helix.nih.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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] The status is being set to Never installed
When I install a tool from the toolshed that has type=set_environment as a requirement, I get this in the main.log: Creating a new record for version None of tool dependency SCRIPT_PATH for revision 5fed38c7e063 of repository mirdeep2. The status is being set to Never installed. Consequently, nothing in the tool_dependency directory is created. The tool is shown to have missing dependencies in the 'Manage installed tool shed repositories' panel. Is there something special that must be done to allow a tool to have only an environment setting as a dependency? Is there something that can be done to fix the problem, other than going into the database and changing the tool_dependency.status from 'Never installed' to 'Installed' and manually creating the subdirectories? David Hoover, PhD Helix Systems Staff ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] display_at_callback
What is the display_at_callback configuration setting, and how does it work? Can it be used as a workaround for remotely authenticated instances of galaxy? David Hoover Helix Systems Staff NIH ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Globus tools for galaxy
Are there any tools available for transferring files using Globus? There’s nothing in the toolsheds, but there was a lot of chatter a few years ago. David Hoover Helix Systems Staff ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] problem with bioc_qvalue, Version: 1.34.0
I saw the same phenomenon. I think it stems from the current version of compute_q_values pointing to unavailable revisions of both R and the bioc_qvalue R package. Whoever maintains the compute_q_values needs to straighten out the revision ids. David Hoover Helix Systems Staff National Institutes of Health On Apr 17, 2014, at 1:38 PM, Tony Kusalik kusa...@cs.usask.ca wrote: Hi, I am having a problem with updating our local Galaxy server, and I am hoping someone can help me. Yesterday I performed a 'hg incoming' command. A bunch of updates were applied, from changeset 12443:ec9d31a8bc04 to changeset 13068:c05752549163. I restarted the server (in daemon mode), but it halted. The content of paster.log instructed me to run sh ./scripts/migrate_tools/0010_tools.sh I did that. That script encountered an error: The following error occurred from the InstallManager while installing tool dependency bioc_qvalue : Error installing tool dependency package bioc_qvalue version 1.34.0: Unable to locate required tool shed repository named package_bioc_qvalue_1_34_0 owned by devteam with revision 11735242a19e. How do I get around this problem? I checked the mailing lists for anyone reporting a problem with bioc_qvalue or 11735242a19e but nothing was turned up. Tony Kusalik ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] jobs stuck in new state
This turned out to be my own ignorance. After creating identical handlers in both universe_wsgi.ini and job_conf.xml, and restarting Galaxy in daemon mode, the jobs became resilient to Galaxy restarts. DOH! Thanks Nate for pointing this out, as well as the limits collection. David On Mar 31, 2014, at 12:20 PM, Ido Tamir ta...@imp.ac.at wrote: In my case it was uncompleted metadata in one of the input files. (but maybe it was not new state but something else?) HTH, ido On Mar 26, 2014, at 5:25 PM, David Hoover hoove...@helix.nih.gov wrote: I have many jobs stuck in the 'new' state on our local Galaxy instance. The jobs can't be stopped using the Admin-Manage jobs tool. First, does anyone know why a job would get stuck in the 'new' state for weeks? I have cleaned things up by manually setting their states to 'error' in the MySQL database. Is there a better way of dealing with 'new' jobs? BTW, our Galaxy instance was updated about two weeks ago. Wondering, David Hoover Helix Systems Staff ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] jobs stuck in new state
I have many jobs stuck in the 'new' state on our local Galaxy instance. The jobs can't be stopped using the Admin-Manage jobs tool. First, does anyone know why a job would get stuck in the 'new' state for weeks? I have cleaned things up by manually setting their states to 'error' in the MySQL database. Is there a better way of dealing with 'new' jobs? BTW, our Galaxy instance was updated about two weeks ago. Wondering, David Hoover Helix Systems Staff ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] restarting Galaxy without affecting jobs
What are the configuration steps required for allowing a local Galaxy installation to be restarted without affecting currently running jobs? I have Galaxy using DRMAA to submit jobs onto a backend cluster. I thought that enable_job_recovery = True should allow this, but in a few tests I have found that although the batch jobs completed, Galaxy lost track of the jobs and classified them as failed. Would track_jobs_in_database = True be required? This is currently set to the default 'None'. Our local Galaxy installation has become quite busy, and restarts are not possible without forcing users to restart their jobs. David Hoover Helix Systems Staff ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] numpy and scipy
Are numpy and scipy included with the standard python modules/eggs supplied by galaxy? David Hoover Helix Systems Staff ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] error with unicode output
Adding ?charset=utf8 to the connection string worked! However, there is one really weird side effect that probably has nothing to do with utf8. The tool creates two pdf files and one zip file as output. For the two pdf files, the expansion of the dataset in the history bar shows 'Image in pdf format'. The zip file shows gobbledygook. How do I tell Galaxy to recognize zip format and not try to parse/head it? Thanks John! On Dec 5, 2013, at 5:03 PM, John Chilton wrote: Hmmm... can you try adding ?charset=utf8 to your database connection string - that may fix the problem? If not - is there a way to tell if the actual columns have changed. Some comments on stackoverflow make it sound like the commands you listed will only affect new columns. Can you try the CONVERT TO CHARACTER SET. ALTER TABLE tbl_name CONVERT TO CHARACTER SET utf8 COLLATE utf8_general_ci; I don't think the problem is sqlalchemy right - this works for postgres and sqlite I believe - it is either that MySQL cannot store UTF-8 data in that column or there is a problem in the mysql connector. It is not clear to me where the problem is based on your stack trace and explanation. I would be happy to work around a limitation in the mysql connector by adding a config option to Galaxy if I were certain that there was a bug in the mysql connector. -John On Thu, Dec 5, 2013 at 12:55 PM, David Hoover hoove...@helix.nih.gov wrote: John, I stopped galaxy, then ran ALTER DATABASE galaxydb DEFAULT CHARACTER SET = 'utf8', then ran ALTER TABLE `[table]` DEFAULT CHARACTER SET = 'utf8' on all the tables in galaxydb. After starting up galaxy and rerunning the jobs (using the unaltered version of lib/galaxy/util/__init__.py), the job failed with the same error. Can I configure the sqlalchemy connection to use utf8? Or must I reconfigure the entire server to use utf8? --David On Dec 5, 2013, at 1:32 PM, John Chilton wrote: Fantastic! For this particular problem - I guess you don't strictly need to modify more than just job and maybe task tables. I suspect at some point there will be a non-latin-1 job parameter or history name or username, etc... that will result in a similar problem though - so if you could just make it all UTF-8 that would probably be ideal. -John On Thu, Dec 5, 2013 at 12:01 PM, David Hoover hoove...@helix.nih.gov wrote: Right, nevermind, 'hg log' listed that changeset 10953:e786022dc67e. Changing DEFAULT_ENCODING to 'latin-1' in lib/galaxy/util/__init__.py worked. Do I need to alter ALL the MySQL tables to UTF-8, or just a selection of tables? Will future updates explicitly create new tables with CHARSET=utf-8, or do I need to reconfigure MySQL to have a new default? -- David On Dec 5, 2013, at 12:32 PM, John Chilton wrote: Actually, can you verify that this commit https://bitbucket.org/galaxy/galaxy-central/commits/e786022dc67ed918050bd81b9ac679ac958e4f75 is in your distribution and if it is try changing: DEFAULT_ENCODING = 'utf-8' in lib/galaxy/util.py to DEFAULT_ENCODING = 'latin-1' If that works then - I can create a database_encoding_default option in universe_wsgi.ini and let you switch it to latin-1 instead of needing to patch Galaxy. Otherwise, setting the MySQL tables to be UTF-8 is probably the better approach - though again - backup and test before applying that change in production. Hope this helps, -John On Thu, Dec 5, 2013 at 11:17 AM, John Chilton chil...@msi.umn.edu wrote: David, Christian, Very sorry about this - this is probably related to fixing some other errors - http://dev.list.galaxyproject.org/Unicode-in-tool-stderr-crashing-galaxy-tt4661749.html#a4661750. I will try to look into this. Christian - what database are targeting? Is it MySQL as well? David - do you have a test setup you can hack on? I wonder if this would go away if you converted your tables to UTF-8. http://stackoverflow.com/questions/6115612/how-to-convert-an-entire-mysql-database-characterset-and-collation-to-utf-8 That is not my official recommendation though - I need to do some more research first. -John On Thu, Dec 5, 2013 at 11:04 AM, Christian Hundsrucker christian.hundsruc...@fmi.ch wrote: Hi David, hi all! I have a similar/the same issue in another setting... galaxy/galaxy_dist/lib/galaxy/jobs/runners/local.py, line 116, in queue_job job_wrapper.finish( stdout, stderr, exit_code ) [...] galaxy/galaxy_dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/persistence.py, line 485, in _emit_update_statements [...] UnicodeEncodeError: 'latin-1' codec can't encode character u'\u2018' in position 134: ordinal not in range(256) I am integrating a set of R/Bioconductor modules into our local Galaxy instance. To do so, I use the discard_stderr_wrapper.sh. It worked fine until the recent update* As the error appears upon any R-output (via print, cat
[galaxy-dev] error with unicode output
I have installed the ngsplot galaxy tool from http://code.google.com/p/ngsplot. This tool creates a set of three pdf files. In older versions of Galaxy, the tool ran correctly with no problems. A recent update broke the tool. The job runs but is unable to finish. Here is the error reported: Traceback (most recent call last): File /spin1/users/galaxy/galaxy/lib/galaxy/jobs/runners/local.py, line 116, in queue_job job_wrapper.finish( stdout, stderr, exit_code ) File /spin1/users/galaxy/galaxy/lib/galaxy/jobs/__init__.py, line 1015, in finish self.sa_session.flush() File build/bdist.linux-x86_64/egg/sqlalchemy/orm/scoping.py, line 114, in do return getattr(self.registry(), name)(*args, **kwargs) File build/bdist.linux-x86_64/egg/sqlalchemy/orm/session.py, line 1718, in flush self._flush(objects) File build/bdist.linux-x86_64/egg/sqlalchemy/orm/session.py, line 1789, in _flush flush_context.execute() File build/bdist.linux-x86_64/egg/sqlalchemy/orm/unitofwork.py, line 331, in execute rec.execute(self) File build/bdist.linux-x86_64/egg/sqlalchemy/orm/unitofwork.py, line 475, in execute uow File build/bdist.linux-x86_64/egg/sqlalchemy/orm/persistence.py, line 59, in save_obj mapper, table, update) File build/bdist.linux-x86_64/egg/sqlalchemy/orm/persistence.py, line 485, in _emit_update_statements execute(statement, params) File build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py, line 1449, in execute params) File build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py, line 1584, in _execute_clauseelement compiled_sql, distilled_params File build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py, line 1691, in _execute_context context) File build/bdist.linux-x86_64/egg/sqlalchemy/engine/default.py, line 331, in do_execute cursor.execute(statement, parameters) File build/bdist.linux-x86_64/egg/MySQLdb/cursors.py, line 158, in execute query = query % db.literal(args) File build/bdist.linux-x86_64/egg/MySQLdb/connections.py, line 265, in literal return self.escape(o, self.encoders) File build/bdist.linux-x86_64/egg/MySQLdb/connections.py, line 203, in unicode_literal return db.literal(u.encode(unicode_literal.charset)) UnicodeEncodeError: 'latin-1' codec can't encode character u'\ufffd' in position 11: ordinal not in range(256) There is a set of files created in the job_working_directory that start with 'metadata_', some of which contain the unicode. Is there anything I can do to fix this? David Hoover Helix Systems Staff ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] error with unicode output
My version is 11216:c458a0fe1ba8. Does this cover the commit? On Dec 5, 2013, at 12:32 PM, John Chilton wrote: Actually, can you verify that this commit https://bitbucket.org/galaxy/galaxy-central/commits/e786022dc67ed918050bd81b9ac679ac958e4f75 is in your distribution and if it is try changing: DEFAULT_ENCODING = 'utf-8' in lib/galaxy/util.py to DEFAULT_ENCODING = 'latin-1' If that works then - I can create a database_encoding_default option in universe_wsgi.ini and let you switch it to latin-1 instead of needing to patch Galaxy. Otherwise, setting the MySQL tables to be UTF-8 is probably the better approach - though again - backup and test before applying that change in production. Hope this helps, -John On Thu, Dec 5, 2013 at 11:17 AM, John Chilton chil...@msi.umn.edu wrote: David, Christian, Very sorry about this - this is probably related to fixing some other errors - http://dev.list.galaxyproject.org/Unicode-in-tool-stderr-crashing-galaxy-tt4661749.html#a4661750. I will try to look into this. Christian - what database are targeting? Is it MySQL as well? David - do you have a test setup you can hack on? I wonder if this would go away if you converted your tables to UTF-8. http://stackoverflow.com/questions/6115612/how-to-convert-an-entire-mysql-database-characterset-and-collation-to-utf-8 That is not my official recommendation though - I need to do some more research first. -John On Thu, Dec 5, 2013 at 11:04 AM, Christian Hundsrucker christian.hundsruc...@fmi.ch wrote: Hi David, hi all! I have a similar/the same issue in another setting... galaxy/galaxy_dist/lib/galaxy/jobs/runners/local.py, line 116, in queue_job job_wrapper.finish( stdout, stderr, exit_code ) [...] galaxy/galaxy_dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/persistence.py, line 485, in _emit_update_statements [...] UnicodeEncodeError: 'latin-1' codec can't encode character u'\u2018' in position 134: ordinal not in range(256) I am integrating a set of R/Bioconductor modules into our local Galaxy instance. To do so, I use the discard_stderr_wrapper.sh. It worked fine until the recent update* As the error appears upon any R-output (via print, cat or error channel), I just set the option -v for the cat command in the discard_stderr_wrapper.sh: cat $TMPFILE 2 = cat -v $TMPFILE 2 as a temporary workaround. No idea if this is applicable in your case?! Cheers, Christian * changeset: 11219:5c789ab4144a branch: stable tag: tip On 05.12.2013 17:29, David Hoover wrote: I have installed the ngsplot galaxy tool from http://code.google.com/p/ngsplot. This tool creates a set of three pdf files. In older versions of Galaxy, the tool ran correctly with no problems. A recent update broke the tool. The job runs but is unable to finish. Here is the error reported: Traceback (most recent call last): File /spin1/users/galaxy/galaxy/lib/galaxy/jobs/runners/local.py, line 116, in queue_job job_wrapper.finish( stdout, stderr, exit_code ) File /spin1/users/galaxy/galaxy/lib/galaxy/jobs/__init__.py, line 1015, in finish self.sa_session.flush() File build/bdist.linux-x86_64/egg/sqlalchemy/orm/scoping.py, line 114, in do return getattr(self.registry(), name)(*args, **kwargs) File build/bdist.linux-x86_64/egg/sqlalchemy/orm/session.py, line 1718, in flush self._flush(objects) File build/bdist.linux-x86_64/egg/sqlalchemy/orm/session.py, line 1789, in _flush flush_context.execute() File build/bdist.linux-x86_64/egg/sqlalchemy/orm/unitofwork.py, line 331, in execute rec.execute(self) File build/bdist.linux-x86_64/egg/sqlalchemy/orm/unitofwork.py, line 475, in execute uow File build/bdist.linux-x86_64/egg/sqlalchemy/orm/persistence.py, line 59, in save_obj mapper, table, update) File build/bdist.linux-x86_64/egg/sqlalchemy/orm/persistence.py, line 485, in _emit_update_statements execute(statement, params) File build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py, line 1449, in execute params) File build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py, line 1584, in _execute_clauseelement compiled_sql, distilled_params File build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py, line 1691, in _execute_context context) File build/bdist.linux-x86_64/egg/sqlalchemy/engine/default.py, line 331, in do_execute cursor.execute(statement, parameters) File build/bdist.linux-x86_64/egg/MySQLdb/cursors.py, line 158, in execute query = query % db.literal(args) File build/bdist.linux-x86_64/egg/MySQLdb/connections.py, line 265, in literal return self.escape(o, self.encoders) File build/bdist.linux-x86_64/egg/MySQLdb/connections.py, line 203, in unicode_literal return db.literal(u.encode(unicode_literal.charset)) UnicodeEncodeError: 'latin-1' codec can't encode character u'\ufffd' in position
Re: [galaxy-dev] error with unicode output
Right, nevermind, 'hg log' listed that changeset 10953:e786022dc67e. Changing DEFAULT_ENCODING to 'latin-1' in lib/galaxy/util/__init__.py worked. Do I need to alter ALL the MySQL tables to UTF-8, or just a selection of tables? Will future updates explicitly create new tables with CHARSET=utf-8, or do I need to reconfigure MySQL to have a new default? -- David On Dec 5, 2013, at 12:32 PM, John Chilton wrote: Actually, can you verify that this commit https://bitbucket.org/galaxy/galaxy-central/commits/e786022dc67ed918050bd81b9ac679ac958e4f75 is in your distribution and if it is try changing: DEFAULT_ENCODING = 'utf-8' in lib/galaxy/util.py to DEFAULT_ENCODING = 'latin-1' If that works then - I can create a database_encoding_default option in universe_wsgi.ini and let you switch it to latin-1 instead of needing to patch Galaxy. Otherwise, setting the MySQL tables to be UTF-8 is probably the better approach - though again - backup and test before applying that change in production. Hope this helps, -John On Thu, Dec 5, 2013 at 11:17 AM, John Chilton chil...@msi.umn.edu wrote: David, Christian, Very sorry about this - this is probably related to fixing some other errors - http://dev.list.galaxyproject.org/Unicode-in-tool-stderr-crashing-galaxy-tt4661749.html#a4661750. I will try to look into this. Christian - what database are targeting? Is it MySQL as well? David - do you have a test setup you can hack on? I wonder if this would go away if you converted your tables to UTF-8. http://stackoverflow.com/questions/6115612/how-to-convert-an-entire-mysql-database-characterset-and-collation-to-utf-8 That is not my official recommendation though - I need to do some more research first. -John On Thu, Dec 5, 2013 at 11:04 AM, Christian Hundsrucker christian.hundsruc...@fmi.ch wrote: Hi David, hi all! I have a similar/the same issue in another setting... galaxy/galaxy_dist/lib/galaxy/jobs/runners/local.py, line 116, in queue_job job_wrapper.finish( stdout, stderr, exit_code ) [...] galaxy/galaxy_dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/persistence.py, line 485, in _emit_update_statements [...] UnicodeEncodeError: 'latin-1' codec can't encode character u'\u2018' in position 134: ordinal not in range(256) I am integrating a set of R/Bioconductor modules into our local Galaxy instance. To do so, I use the discard_stderr_wrapper.sh. It worked fine until the recent update* As the error appears upon any R-output (via print, cat or error channel), I just set the option -v for the cat command in the discard_stderr_wrapper.sh: cat $TMPFILE 2 = cat -v $TMPFILE 2 as a temporary workaround. No idea if this is applicable in your case?! Cheers, Christian * changeset: 11219:5c789ab4144a branch: stable tag: tip On 05.12.2013 17:29, David Hoover wrote: I have installed the ngsplot galaxy tool from http://code.google.com/p/ngsplot. This tool creates a set of three pdf files. In older versions of Galaxy, the tool ran correctly with no problems. A recent update broke the tool. The job runs but is unable to finish. Here is the error reported: Traceback (most recent call last): File /spin1/users/galaxy/galaxy/lib/galaxy/jobs/runners/local.py, line 116, in queue_job job_wrapper.finish( stdout, stderr, exit_code ) File /spin1/users/galaxy/galaxy/lib/galaxy/jobs/__init__.py, line 1015, in finish self.sa_session.flush() File build/bdist.linux-x86_64/egg/sqlalchemy/orm/scoping.py, line 114, in do return getattr(self.registry(), name)(*args, **kwargs) File build/bdist.linux-x86_64/egg/sqlalchemy/orm/session.py, line 1718, in flush self._flush(objects) File build/bdist.linux-x86_64/egg/sqlalchemy/orm/session.py, line 1789, in _flush flush_context.execute() File build/bdist.linux-x86_64/egg/sqlalchemy/orm/unitofwork.py, line 331, in execute rec.execute(self) File build/bdist.linux-x86_64/egg/sqlalchemy/orm/unitofwork.py, line 475, in execute uow File build/bdist.linux-x86_64/egg/sqlalchemy/orm/persistence.py, line 59, in save_obj mapper, table, update) File build/bdist.linux-x86_64/egg/sqlalchemy/orm/persistence.py, line 485, in _emit_update_statements execute(statement, params) File build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py, line 1449, in execute params) File build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py, line 1584, in _execute_clauseelement compiled_sql, distilled_params File build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py, line 1691, in _execute_context context) File build/bdist.linux-x86_64/egg/sqlalchemy/engine/default.py, line 331, in do_execute cursor.execute(statement, parameters) File build/bdist.linux-x86_64/egg/MySQLdb/cursors.py, line 158, in execute query = query % db.literal(args) File build/bdist.linux-x86_64/egg/MySQLdb
Re: [galaxy-dev] error with unicode output
John, I stopped galaxy, then ran ALTER DATABASE galaxydb DEFAULT CHARACTER SET = 'utf8', then ran ALTER TABLE `[table]` DEFAULT CHARACTER SET = 'utf8' on all the tables in galaxydb. After starting up galaxy and rerunning the jobs (using the unaltered version of lib/galaxy/util/__init__.py), the job failed with the same error. Can I configure the sqlalchemy connection to use utf8? Or must I reconfigure the entire server to use utf8? --David On Dec 5, 2013, at 1:32 PM, John Chilton wrote: Fantastic! For this particular problem - I guess you don't strictly need to modify more than just job and maybe task tables. I suspect at some point there will be a non-latin-1 job parameter or history name or username, etc... that will result in a similar problem though - so if you could just make it all UTF-8 that would probably be ideal. -John On Thu, Dec 5, 2013 at 12:01 PM, David Hoover hoove...@helix.nih.gov wrote: Right, nevermind, 'hg log' listed that changeset 10953:e786022dc67e. Changing DEFAULT_ENCODING to 'latin-1' in lib/galaxy/util/__init__.py worked. Do I need to alter ALL the MySQL tables to UTF-8, or just a selection of tables? Will future updates explicitly create new tables with CHARSET=utf-8, or do I need to reconfigure MySQL to have a new default? -- David On Dec 5, 2013, at 12:32 PM, John Chilton wrote: Actually, can you verify that this commit https://bitbucket.org/galaxy/galaxy-central/commits/e786022dc67ed918050bd81b9ac679ac958e4f75 is in your distribution and if it is try changing: DEFAULT_ENCODING = 'utf-8' in lib/galaxy/util.py to DEFAULT_ENCODING = 'latin-1' If that works then - I can create a database_encoding_default option in universe_wsgi.ini and let you switch it to latin-1 instead of needing to patch Galaxy. Otherwise, setting the MySQL tables to be UTF-8 is probably the better approach - though again - backup and test before applying that change in production. Hope this helps, -John On Thu, Dec 5, 2013 at 11:17 AM, John Chilton chil...@msi.umn.edu wrote: David, Christian, Very sorry about this - this is probably related to fixing some other errors - http://dev.list.galaxyproject.org/Unicode-in-tool-stderr-crashing-galaxy-tt4661749.html#a4661750. I will try to look into this. Christian - what database are targeting? Is it MySQL as well? David - do you have a test setup you can hack on? I wonder if this would go away if you converted your tables to UTF-8. http://stackoverflow.com/questions/6115612/how-to-convert-an-entire-mysql-database-characterset-and-collation-to-utf-8 That is not my official recommendation though - I need to do some more research first. -John On Thu, Dec 5, 2013 at 11:04 AM, Christian Hundsrucker christian.hundsruc...@fmi.ch wrote: Hi David, hi all! I have a similar/the same issue in another setting... galaxy/galaxy_dist/lib/galaxy/jobs/runners/local.py, line 116, in queue_job job_wrapper.finish( stdout, stderr, exit_code ) [...] galaxy/galaxy_dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/persistence.py, line 485, in _emit_update_statements [...] UnicodeEncodeError: 'latin-1' codec can't encode character u'\u2018' in position 134: ordinal not in range(256) I am integrating a set of R/Bioconductor modules into our local Galaxy instance. To do so, I use the discard_stderr_wrapper.sh. It worked fine until the recent update* As the error appears upon any R-output (via print, cat or error channel), I just set the option -v for the cat command in the discard_stderr_wrapper.sh: cat $TMPFILE 2 = cat -v $TMPFILE 2 as a temporary workaround. No idea if this is applicable in your case?! Cheers, Christian * changeset: 11219:5c789ab4144a branch: stable tag: tip On 05.12.2013 17:29, David Hoover wrote: I have installed the ngsplot galaxy tool from http://code.google.com/p/ngsplot. This tool creates a set of three pdf files. In older versions of Galaxy, the tool ran correctly with no problems. A recent update broke the tool. The job runs but is unable to finish. Here is the error reported: Traceback (most recent call last): File /spin1/users/galaxy/galaxy/lib/galaxy/jobs/runners/local.py, line 116, in queue_job job_wrapper.finish( stdout, stderr, exit_code ) File /spin1/users/galaxy/galaxy/lib/galaxy/jobs/__init__.py, line 1015, in finish self.sa_session.flush() File build/bdist.linux-x86_64/egg/sqlalchemy/orm/scoping.py, line 114, in do return getattr(self.registry(), name)(*args, **kwargs) File build/bdist.linux-x86_64/egg/sqlalchemy/orm/session.py, line 1718, in flush self._flush(objects) File build/bdist.linux-x86_64/egg/sqlalchemy/orm/session.py, line 1789, in _flush flush_context.execute() File build/bdist.linux-x86_64/egg/sqlalchemy/orm/unitofwork.py, line 331, in execute rec.execute(self) File build/bdist.linux-x86_64/egg
[galaxy-dev] Library permission page broken
After the latest update, the Manage library permissions page is broken. The Roles not associated boxes are pushed to the left of the frame, and the double arrow buttons are misplaced down the page. This occurs under Safari (5.1.10) and Chrome (31.0.1650.57) on a Mac running OS X 10.6.8. Firefox (25.0.1), however, seems ok. ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] FTP bug with automatically decompressed files
When a file is uploaded via FTP, and the file is compressed using gzip, the file is uploaded and decompressed on the fly; however, the gzipped file is left on the FTP server, rather than being deleted as normal. Is this a bug? David Hoover Helix Systems Staff ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] browse directories on galaxy server
Is there any desire to create a way in galaxy to browse local directories on the galaxy server itself? Not the client machine running the web browwser, but the machine on which galaxy is running. I've created a tool that allows a user to upload a single file from their own personal directory on the galaxy server into galaxy directly, without going through Apache. However, this is very limiting. It would be very helpful to be able to browse directories that are deemed accessible to the galaxy user, and before I begin trying to develop anything I'd like to know if there is any support for such a feature. David Hoover Helix Systems Staff National Institutes of Health ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] qa_url = slyfox?
Strangely, I had never noticed this before. On some tools, there is a link at the top of the tool page that attempts to connect to http://slyfox.bx.psu.edu:8080/, which it can't. This URL is set via the qa_url directive in the universe_wsgi.ini file. What is this URL, and what should it be? David Hoover Helix Systems Staff ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] no module named gmap
Hi, I'm trying to load an instance of Galaxy from scratch, and I'm getting this error message after configuration and typing ./run.sh: Traceback (most recent call last): File ./scripts/paster.py, line 33, in module serve.run() File /spin1/users/galaxy/galaxy1/lib/galaxy/util/pastescript/serve.py, line 1056, in run invoke(command, command_name, options, args[1:]) File /spin1/users/galaxy/galaxy1/lib/galaxy/util/pastescript/serve.py, line 1062, in invoke exit_code = runner.run(args) File /spin1/users/galaxy/galaxy1/lib/galaxy/util/pastescript/serve.py, line 227, in run result = self.command() File /spin1/users/galaxy/galaxy1/lib/galaxy/util/pastescript/serve.py, line 650, in command app = loadapp( app_spec, name=app_name, relative_to=base, global_conf=vars) File /spin1/users/galaxy/galaxy1/lib/galaxy/util/pastescript/loadwsgi.py, line 350, in loadapp return loadobj(APP, uri, name=name, **kw) File /spin1/users/galaxy/galaxy1/lib/galaxy/util/pastescript/loadwsgi.py, line 374, in loadobj global_conf=global_conf) File /spin1/users/galaxy/galaxy1/lib/galaxy/util/pastescript/loadwsgi.py, line 399, in loadcontext global_conf=global_conf) File /spin1/users/galaxy/galaxy1/lib/galaxy/util/pastescript/loadwsgi.py, line 423, in _loadconfig return loader.get_context(object_type, name, global_conf) File /spin1/users/galaxy/galaxy1/lib/galaxy/util/pastescript/loadwsgi.py, line 561, in get_context section) File /spin1/users/galaxy/galaxy1/lib/galaxy/util/pastescript/loadwsgi.py, line 620, in _context_from_explicit value = import_string(found_expr) File /spin1/users/galaxy/galaxy1/lib/galaxy/util/pastescript/loadwsgi.py, line 125, in import_string return pkg_resources.EntryPoint.parse(x= + s).load(False) File /spin1/users/galaxy/galaxy1/lib/pkg_resources.py, line 1954, in load entry = __import__(self.module_name, globals(),globals(), ['__name__']) File /spin1/users/galaxy/galaxy1/lib/galaxy/web/buildapp.py, line 3, in module from galaxy.webapps.galaxy.buildapp import app_factory File /spin1/users/galaxy/galaxy1/lib/galaxy/webapps/galaxy/buildapp.py, line 18, in module from galaxy import config, jobs, util, tools File /spin1/users/galaxy/galaxy1/lib/galaxy/jobs/__init__.py, line 15, in module from galaxy import util, model File /spin1/users/galaxy/galaxy1/lib/galaxy/model/__init__.py, line 13, in module import galaxy.datatypes.registry File /spin1/users/galaxy/galaxy1/lib/galaxy/datatypes/registry.py, line 9, in module import gmap # added for gmap tools ImportError: No module named gmap What is missing? David Hoover Helix Systems Staff ___ 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/
Re: [galaxy-dev] no module named gmap
This is a fresh clone, from galaxy-dist, but I have a pile of patch files to keep my local hacks straight. I forgot about the registry.py file. Removed that, as well as the blast import. It's hard to keep local hacks and regular updates in sync... Thanks, David On 3/6/2013 12:16 PM, Dannon Baker wrote: Is this a fresh clone from galaxy-dist or have you pulled it from somewhere else? It looks like your galaxy clone's lib/galaxy/datatypes/registry.py has been altered to have an extra import, 'gmap', for gmap tools. -Dannon On Wed, Mar 6, 2013 at 12:08 PM, David Hoover hoove...@helix.nih.gov mailto:hoove...@helix.nih.gov wrote: Hi, I'm trying to load an instance of Galaxy from scratch, and I'm getting this error message after configuration and typing ./run.sh: Traceback (most recent call last): File ./scripts/paster.py, line 33, in module serve.run() File /spin1/users/galaxy/galaxy1/lib/galaxy/util/pastescript/serve.py, line 1056, in run invoke(command, command_name, options, args[1:]) File /spin1/users/galaxy/galaxy1/lib/galaxy/util/pastescript/serve.py, line 1062, in invoke exit_code = runner.run(args) File /spin1/users/galaxy/galaxy1/lib/galaxy/util/pastescript/serve.py, line 227, in run result = self.command() File /spin1/users/galaxy/galaxy1/lib/galaxy/util/pastescript/serve.py, line 650, in command app = loadapp( app_spec, name=app_name, relative_to=base, global_conf=vars) File /spin1/users/galaxy/galaxy1/lib/galaxy/util/pastescript/loadwsgi.py, line 350, in loadapp return loadobj(APP, uri, name=name, **kw) File /spin1/users/galaxy/galaxy1/lib/galaxy/util/pastescript/loadwsgi.py, line 374, in loadobj global_conf=global_conf) File /spin1/users/galaxy/galaxy1/lib/galaxy/util/pastescript/loadwsgi.py, line 399, in loadcontext global_conf=global_conf) File /spin1/users/galaxy/galaxy1/lib/galaxy/util/pastescript/loadwsgi.py, line 423, in _loadconfig return loader.get_context(object_type, name, global_conf) File /spin1/users/galaxy/galaxy1/lib/galaxy/util/pastescript/loadwsgi.py, line 561, in get_context section) File /spin1/users/galaxy/galaxy1/lib/galaxy/util/pastescript/loadwsgi.py, line 620, in _context_from_explicit value = import_string(found_expr) File /spin1/users/galaxy/galaxy1/lib/galaxy/util/pastescript/loadwsgi.py, line 125, in import_string return pkg_resources.EntryPoint.parse(x= + s).load(False) File /spin1/users/galaxy/galaxy1/lib/pkg_resources.py, line 1954, in load entry = __import__(self.module_name, globals(),globals(), ['__name__']) File /spin1/users/galaxy/galaxy1/lib/galaxy/web/buildapp.py, line 3, in module from galaxy.webapps.galaxy.buildapp import app_factory File /spin1/users/galaxy/galaxy1/lib/galaxy/webapps/galaxy/buildapp.py, line 18, in module from galaxy import config, jobs, util, tools File /spin1/users/galaxy/galaxy1/lib/galaxy/jobs/__init__.py, line 15, in module from galaxy import util, model File /spin1/users/galaxy/galaxy1/lib/galaxy/model/__init__.py, line 13, in module import galaxy.datatypes.registry File /spin1/users/galaxy/galaxy1/lib/galaxy/datatypes/registry.py, line 9, in module import gmap # added for gmap tools ImportError: No module named gmap What is missing? David Hoover Helix Systems Staff ___ 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/ ___ 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/
[galaxy-dev] admin menu column won't scroll
I've installed the latest version of galaxy, and the admin column won't scroll. I can't see any of the toolshed functions unless mybrowser is expanded beyond the size of my desktop display. Is there something wrong? David Hoover Helix Systems Staff ___ 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/
[galaxy-dev] picard bug in Add or Replace Groups
In the Add or Replace Groups tool for picard, if the read group platform unit is left blank, the read group sample name is lost as well. Must all the read group tags be set with this tool? Can some of them remain blank? David Hoover Helix Systems Staff, CIT/NIH ___ 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/
[galaxy-dev] Fwd: fastQC report bug
How should I configure my local galaxy to allow access to sub-files in /datasets/[hashcode]/display/? FastQC is still broken on the latest build. This issue was reported by others as well. David Hoover Helix Systems Staff, CIT/NIH Begin forwarded message: From: David Hoover hoove...@helix.nih.gov Date: September 10, 2012 4:48:30 PM EDT To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] fastQC report bug Hi, I have a very recent version of Galaxy installed locally, and when I run FastQC:Read QC, it creates an HTML file with missing links to the plots and images within the HTML. The HTML source looks identical to the HTML source from the main Galaxy server, so there must be something wrong with my local install. Is there some option or modification that I need to enable to allow access to the generated HTML/PNG files in the database/files/000/database_###_files directory? David Hoover Helix Systems Staff ___ 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/ ___ 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/
[galaxy-dev] trying to set up local toolshed
I'm trying to host a local toolshed, and I've hit a brick wall. It is accessible as a subdirectory under our galaxy installation, uses SQLite as the database, and I've configured it as much as I understand. After I start it up, I can see the main page in the browser, but get this error message: Not Found The resource could not be found. No route for /repository/browse_categories Clicking on 'Repositories' gives this error: This link may not be followed from within Galaxy. Beyond this, can the toolshed use externally authenticated users? David Hoover Helix Systems Staff ___ 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/
Re: [galaxy-dev] submitting jobs as the real user
This script is used multiple times, so you might want to make sure that this change won't cause files to become readable that you would prefer remain unreadable. From the log output, it looks like files are chmod'd to the user, then later back to the Galaxy user. Is there somewhere else that isn't logged? Since you mention Apache uploading, what are you using for Apache to handle the uploads? I don't know, whatever the default mechanism. I'm not using nginx. David ___ 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/
Re: [galaxy-dev] submitting jobs as the real user
While I've got you on the line, do you know why enabling the real user method blanks out the jobName for the PBS job? The jobName is set if the jobs are submitted as the Galaxy user. David On Oct 3, 2012, at 11:03 AM, Nate Coraor wrote: On Oct 3, 2012, at 10:06 AM, David Hoover wrote: This script is used multiple times, so you might want to make sure that this change won't cause files to become readable that you would prefer remain unreadable. From the log output, it looks like files are chmod'd to the user, then later back to the Galaxy user. Is there somewhere else that isn't logged? Hi David, It chowns the entire working directory, I double checked and I don't see anywhere else it runs. But after looking at the code again, I'm surprised this fix works since it shouldn't touch anything in new_file_path. Since you mention Apache uploading, what are you using for Apache to handle the uploads? I don't know, whatever the default mechanism. I'm not using nginx. This would just upload straight through to Galaxy without any special handling by Apache. Tempfiles are created by Galaxy's internal webserver via the FieldStorage monkeypatch in lib/galaxy/web/framework/base.py --nate David ___ 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/
[galaxy-dev] jobName lost when drmaa used with real user use
When I use the real user method for running drmaa jobs as the real user, the jobName value gets lost. It's kind of annoying, but not a show stopper. The other values (outputPath, errorPath, remoteCommand, nativeSpecification, etc.) are all there, but not jobName. This doesn't happen when the drmaa jobs are run using the default Galaxy user. Weird. David Hoover Helix Systems Staff ___ 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/
[galaxy-dev] where are the tools?
I just recently updated to the latest version of galaxy-central, and when I started galaxy, the tools were not listed on the left panel. I could rerun old jobs from my history, however. Why are the tools not listed? David Hoover Helix Systems Staff ___ 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/
[galaxy-dev] environment variables and paths for toolshed tools
Are there any environment variables that are honored by toolshed installed
tools? I tried creating a tool that uses ${GALAXY_DATA_INDEX_DIR} or
$GALAXY_HOME, then uploaded it the test toolshed, then installed it
automatically. Neither of these resolved to what I expected. I don't want to
hard-code the path in the xml tool file, but rather have a default location for
other executables and jar files. How should this best be done?
David Hoover
Helix Systems Staff
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[galaxy-dev] GATK v2.x
Is anyone working on adapting the GATK tools for a more recent version of GATK? The distributed version is 1.4, and GATK is up to 2.1. David Hoover Helix Systems Staff ___ 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/
[galaxy-dev] fastQC report bug
Hi, I have a very recent version of Galaxy installed locally, and when I run FastQC:Read QC, it creates an HTML file with missing links to the plots and images within the HTML. The HTML source looks identical to the HTML source from the main Galaxy server, so there must be something wrong with my local install. Is there some option or modification that I need to enable to allow access to the generated HTML/PNG files in the database/files/000/database_###_files directory? David Hoover Helix Systems Staff ___ 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/
Re: [galaxy-dev] configuring job runner for toolshed tools
Back on the topic again, I found another real issue with toolshed tools. I can configure the toolshed tool to be used by drmaa in universe_wsgi.ini, then restart Galaxy and everything's good. However, if I modify the tool .xml file and reload it using the Admin link, it goes back to the default job runner. Can this be changed so that the configured job runner remains the same after reloading the toolshed tool? On Jul 23, 2012, at 5:02 PM, David Hoover wrote: OK, forget what I said earlier. I was watching for a different toolshed tool than what I reconfigured. Never mind, using the guid (the long tool_id shown as an example below) worked correctly. The job was pushed out to the cluster and finished normally. Sorry about the fuss. David On Jul 21, 2012, at 8:40 AM, Greg Von Kuster wrote: Hi David, If using the actual tool id (guid) does not work, then it's likely that the job runner code needs to be fixed to correctly handle tools installed from a tool shed. I've created a ticket to get this resolved which you can follow so that you'll receive status changes on the issue. https://bitbucket.org/galaxy/galaxy-central/issue/779/fix-job-runner-to-handle-tools-installed Thanks for reporting this, and sorry for the inconvenience. Greg Von Kuster On Jul 21, 2012, at 8:29 AM, hoove...@helix.nih.gov wrote: I found the guid for the tool and tried the usual method of configuring galaxy to use it via drmaa. With your example, it would be toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/0.0.2 = drmaa://-l nodes=1/ But this didn't have any effect. It still ran on the localhost. I guess no one has tried this. I haven't tried using the old_id. Would that work? I'd rather not run everything via drmaa, but if the toolshed tools can't be configured, I might have to. David Hi David, I'm not familiar enough with the job runners to know what the problem may be, However, for tools installed from the tool shed, the tool id is the tool-shed generated guid instead of the id attribute value of the tool config's tool tag. So, for example, if you install the freebayes tool shed repository from the main Galaxy tool shed, your tool panel will display the single freebayes tool, which is the only tool contained in the freebayes repository. When this installed tool is loaded into Galaxy, the tools id attribute value is: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/0.0.2 and the tool's old_id attribute value is the value os the id attribute in it's tool config tool tag: freebayes Have your tried configuring the installed tool using the new id (guid) rather than the old id? I'm not sure if this works, but just wanted to make sure you were using the correct id value. If it still doesn't work, let us know and we'll get a fix asap. Thanks! Greg Von Kuster On Jul 20, 2012, at 5:16 PM, David Hoover wrote: Is there a way to configure a tool downloaded from the toolshed depot to use a job runner other than the local runner? The tool_id for the toolshed tool isn't honored in universe_wsgi.ini the way the default tools are. Specifically, has anyone configured a toolshed tool to use drmaa instead of localhost? David Hoover Helix Systems Staff ___ 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/ ___ 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/ ___ 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/
[galaxy-dev] annoying bug when deleting datasets
I recently switched from galaxy-dist to galaxy-central as the source of my local install (version 7427:cb9272041d95). When I delete a dataset from a history, all the delete icons disappear from the datasets. They come back if I refresh the page. Has anyone else noticed this? David Hoover Helix Systems Staff ___ 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/
Re: [galaxy-dev] configuring job runner for toolshed tools
OK, forget what I said earlier. I was watching for a different toolshed tool than what I reconfigured. Never mind, using the guid (the long tool_id shown as an example below) worked correctly. The job was pushed out to the cluster and finished normally. Sorry about the fuss. David On Jul 21, 2012, at 8:40 AM, Greg Von Kuster wrote: Hi David, If using the actual tool id (guid) does not work, then it's likely that the job runner code needs to be fixed to correctly handle tools installed from a tool shed. I've created a ticket to get this resolved which you can follow so that you'll receive status changes on the issue. https://bitbucket.org/galaxy/galaxy-central/issue/779/fix-job-runner-to-handle-tools-installed Thanks for reporting this, and sorry for the inconvenience. Greg Von Kuster On Jul 21, 2012, at 8:29 AM, hoove...@helix.nih.gov wrote: I found the guid for the tool and tried the usual method of configuring galaxy to use it via drmaa. With your example, it would be toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/0.0.2 = drmaa://-l nodes=1/ But this didn't have any effect. It still ran on the localhost. I guess no one has tried this. I haven't tried using the old_id. Would that work? I'd rather not run everything via drmaa, but if the toolshed tools can't be configured, I might have to. David Hi David, I'm not familiar enough with the job runners to know what the problem may be, However, for tools installed from the tool shed, the tool id is the tool-shed generated guid instead of the id attribute value of the tool config's tool tag. So, for example, if you install the freebayes tool shed repository from the main Galaxy tool shed, your tool panel will display the single freebayes tool, which is the only tool contained in the freebayes repository. When this installed tool is loaded into Galaxy, the tools id attribute value is: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/0.0.2 and the tool's old_id attribute value is the value os the id attribute in it's tool config tool tag: freebayes Have your tried configuring the installed tool using the new id (guid) rather than the old id? I'm not sure if this works, but just wanted to make sure you were using the correct id value. If it still doesn't work, let us know and we'll get a fix asap. Thanks! Greg Von Kuster On Jul 20, 2012, at 5:16 PM, David Hoover wrote: Is there a way to configure a tool downloaded from the toolshed depot to use a job runner other than the local runner? The tool_id for the toolshed tool isn't honored in universe_wsgi.ini the way the default tools are. Specifically, has anyone configured a toolshed tool to use drmaa instead of localhost? David Hoover Helix Systems Staff ___ 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/ ___ 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/
[galaxy-dev] configuring job runner for toolshed tools
Is there a way to configure a tool downloaded from the toolshed depot to use a job runner other than the local runner? The tool_id for the toolshed tool isn't honored in universe_wsgi.ini the way the default tools are. Specifically, has anyone configured a toolshed tool to use drmaa instead of localhost? David Hoover Helix Systems Staff ___ 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/
[galaxy-dev] migrate ownership of galaxy user
I have a somewhat unusual problem. I have a local instance of Galaxy wherein users are created automatically upon authentication (use_remote_user = True). However, for a handful of users, their remote_user names have changed. After that change, a new Galaxy user and role were created, and they can't access their old data. Worse, they continued using the new account and so now have two sets of (possibly) identical data. Is there a simple way of migrating datasets, jobs, quotas, etc., from one user to another? I've figured out a way to make the necessary changes at the MySQL database level. However, there is one sticky problem. None of the tables (aside from role and galaxy_user) define the role_id or the user_id as unique, so I would assume I can simply UPDATE the table to set the old role_id or user_id to the new role_id or user_id. Unfortunately, it appears that some of the tables are in practice keeping the role_id or user_id as unique. For example, default_user_permissions or user_role_association. Could a single user have multiple default permissions or multiple roles? What would happen if this were the case? In short, can anyone say which tables have practical unique role_id/user_id to data associations? Of course, I could just delete the old user and say too bad... Thanks, David Hoover Helix Systems Staff, CIT/NIH ___ 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/
Re: [galaxy-dev] Error for draw quality score boxplot
You first need to find where on your Galaxy server the fonts are for gnuplot. An example is /usr/local/share/fonts/msttcorefonts. Once you know the directory, you can set an environment variable for your Galaxy user, like this: export GDFONTPATH=/usr/local/share/fonts/msttcorefonts Place this in the .bashrc file for the Galaxy user then restart your server. David Hoover Helix Systems Staff, NIH On Mar 27, 2012, at 4:31 PM, Xu, Jianpeng wrote: Hi, I have installed the local galaxy and tried to run draw quality score boxplot. It showed the error message: Could not find/open font when opening font arial, using internal non-scalable font Could you please tell me how to fix it ? Thanks, Jianpeng 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). ___ 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/ ___ 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/
[galaxy-dev] limited tool shed browse
When I click on Admin-'Search and browse tool sheds'-'Galaxy main tool shed', it shows the first page of Valid repositories. However, clicking '2', '3', '4', or 'Show All' has no effect. I can only display the first page of repositories. However, if I search for valid tools using the menu under 'Galaxy main tool shed', I can get to any of the repositories listed at the Galaxy main toolshed. Is this a bug or a feature? David Hoover Helix Systems Staff ___ 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/
Re: [galaxy-dev] Unix user account/connection and Galaxy connection
I'd love to know answers to this question as well. So far, all I've done is create two tools for copying files between Galaxy and a user's personal directories using a rather dangerous setuid executable. I have mulled over two possibilities for this problem. One is to run Galaxy as root. The other is for each user to kick off their own personal instance of Galaxy as themselves, but accessing the same main database and file repository. The latter would require all files be read-write accesible to all users. Neither is good. On Jan 30, 2012, at 4:29 AM, Sarah Maman wrote: Dear all, There is currently no link between an user ssh connection on his own account (own space on Unix) and the Galaxy connection. How to run Galaxy on an Unix user account? How to link the data storage system and the Unix user account (symlink?)? The goal is to not need to copy or move data. PS : Thanks a lot to David, Gordon, Brad, Christophe and Nate for your help on LDAP authentification. I always try to find a solution (Apache configuration). I will inform Galaxy list when I will find a solution. Thanks in advance, Sarah ___ 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/
Re: [galaxy-dev] LDAP authentification
Why do you need to create a proxy? The way I have ours set up is within a
virtual host:
VirtualHost
Location /
AuthName Helix Systems
AuthType Basic
AuthBasicProvider ldap
AuthzLDAPAuthoritative off
AuthLDAPUrl ldaps://helixdrive.nih.gov/ou=Users,ou=helix.nih.gov,o=scb?uid
AuthLDAPBindDN cn=maccount,ou=Special,o=scb
AuthLDAPBindPassword
Require valid-user
RequestHeader set REMOTE_USER %{AUTHENTICATE_uid}e
Options None
Order Allow,Deny
Allow from all
/Location
RewriteRule ^/static/style/(.*)
/data/galaxy/pro/static/june_2007_style/blue/$1 [L]
RewriteRule ^/static/scripts/(.*) /data/galaxy/pro/static/scripts/packed/$1
[L]
RewriteRule ^/static/(.*) /data/galaxy/pro/static/$1 [L]
RewriteRule ^/favicon.ico /data/galaxy/pro/static/favicon.ico [L]
RewriteRule ^/robots.txt /data/galaxy/pro/static/robots.txt [L]
RewriteRule ^(.*) http://helixweb4.cit.nih.gov:8080$1 [P]
/VirtualHost
David
On Jan 19, 2012, at 10:49 AM, Sarah Maman wrote:
Hi Brad, Hi Christopher,
Thanks a lot.
I'm talking to Open LDAP. I have changed
RequestHeader set REMOTE_USER %{AUTHENTICATE_uid}e
to
RequestHeader set REMOTE_USER %{AUTHENTICATE_UID}e
But I always have the same message /(Access to Galaxy is denied
Galaxy is configured to authenticate users via an external method (such as
HTTP authentication in Apache), but a username was not provided by the
upstream (proxy) server. This is generally due to a misconfiguration in the
upstream server. )/
This is my .conf file :
Proxy http://localhost:8080
Order deny,allow
Allow from all
/Proxy
RewriteEngine on
Location /
AuthType Basic
AuthName Galaxy
AuthBasicProvider ldap
AuthLDAPURL
ldap://server/ou=People,ou=genopole,ou=toulouse,o=inra,c=fr?u
id?sub?(objectClass=person)
AuthzLDAPAuthoritative off
Require valid-user
# Take the $REMOTE_USER environment variable and set it as a
header in the proxy request.
#RewriteCond %{IS_SUBREQ} ^false$
#RewriteCond %{LA-U:REMOTE_USER} (.+)
#RewriteRule . - [E=RU:%1]
#RequestHeader set REMOTE_USER %{RU}e
RequestHeader set REMOTE_USER %{AUTHENTICATE_UID}e
/Location
Thanks in advance,
Sarah
Langhorst, Brad a écrit :
Hi Sarah:
I don't know what kind of LDAP you're talking to... I'm talking to Active
Directory and this configuration works in that situation.
Order allow,deny
allow from all
AuthType Basic
AuthName NEB Credentials
AuthBasicProvider ldap
AuthzLDAPAuthoritative off
AuthLDAPBindDN ccaloo...@neb.com
AuthLDAPBindPassword password
AuthLDAPURL
ldap://ldap.domain.com:389/dc=domain,dc=com?sAMAccountName
require valid-user
RewriteCond %{IS_SUBREQ} ^false$
RewriteCond %{LA-U:REMOTE_USER} (.+)
RewriteRule . - [E=RU:%1]
RequestHeader set REMOTE_USER
%{AUTHENTICATE_sAMAccountName}e
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Re: [galaxy-dev] scatterplot broken
Again, solved my own problem. diff -r 949e4f5fa03a tools/plotting/scatterplot.py --- a/tools/plotting/scatterplot.py Mon Aug 29 14:42:04 2011 -0400 +++ b/tools/plotting/scatterplot.py Wed Oct 12 10:35:58 2011 -0400 @@ -20,7 +20,8 @@ xlab = sys.argv[6] ylab = sys.argv[7] -matrix = [] +xarray = [] +yarray = [] skipped_lines = 0 first_invalid_line = 0 invalid_value = '' @@ -57,12 +58,13 @@ first_invalid_line = i+1 if valid: -matrix.append( row ) +xarray.append ( row[0] ) +yarray.append ( row[1] ) if skipped_lines i: try: r.pdf( out_fname, 8, 8 ) -r.plot( array( matrix ), type=p, main=title, xlab=xlab, ylab=ylab, col=blue, pch=19 ) +r.plot( xarray, yarray, type=p, main=title, xlab=xlab, ylab=ylab, col=blue, pch=19 ) r.dev_off() except Exception, exc: stop_err( %s %str( exc ) ) David On Oct 6, 2011, at 10:16 AM, David Hoover wrote: Hi, The scatterplot tool is broken in the distributed version. It works on the main Galaxy server, but on our local installation it gives this error: An error occurred running this job:Warning messages: 1: In min(x) : no non-missing arguments to min; returning Inf 2: In max(x) : no non-missing arguments to max; returning -Inf 3: In min(x) : no non-missing arguments to min; returning Inf 4: In max(x) : no non-missing arguments to max; re Any ideas? David Hoover Helix Systems Staff SCB/CIT/NIH ___ 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/ ___ 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/
[galaxy-dev] scatterplot broken
Hi, The scatterplot tool is broken in the distributed version. It works on the main Galaxy server, but on our local installation it gives this error: An error occurred running this job:Warning messages: 1: In min(x) : no non-missing arguments to min; returning Inf 2: In max(x) : no non-missing arguments to max; returning -Inf 3: In min(x) : no non-missing arguments to min; returning Inf 4: In max(x) : no non-missing arguments to max; re Any ideas? David Hoover Helix Systems Staff SCB/CIT/NIH ___ 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/
Re: [galaxy-dev] prevent downloaded files with .txt added
I apologize for responding to my own email, but I thought others might want to know. This turned out to be a Safari-dependent problem. Lots of other people have complained, but there doesn't seem to be any direct fix. My quick solution was to make sure the downloaded file is gzipped. This kills two birds with one stone -- the download is smaller, and Safari doesn't mess with the extension. Now, does anyone know if it is possible to gzip a dataset from a history within Galaxy prior to downloading? David On Sep 26, 2011, at 2:00 PM, David Hoover wrote: Does anyone know how to prevent the .txt suffix from being added to files downloaded from Galaxy? For example, a fasta file is downloaded as xxx.fasta.txt, instead of xxx.fasta. Wondering, David Hoover Helix Systems Staff http://helix.nih.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/ ___ 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/
[galaxy-dev] samtools mpileup update
Is there any good reason why Galaxy can't use a more recent version of samtools? The only difference I can see is the mpileup command. The algorithm by which mpileup finds SNPs is a little different. Does anyone know if the file format has changed? The only files that need to change are sam_pileup.py and sam_pileup.xml. David Hoover Helix Systems Staff http://helix.nih.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/
[galaxy-dev] substitute or replace a value?
Is there a tool for doing a global or column-based substitution in a text or tabular file? For example, replace all instances of the number 2 in a column to a number 1? David Hoover Helix Systems Staff http://helix.nih.gov ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] megablast and blastdb
When I try to load the megablast_wrapper tool, I get errors in the output: AssertionError: Data table named 'blastdb' is required by tool but not configured I am totally confused how blastdb.loc should be configured. Is it one tab, two, three? David Hoover Helix Systems Staff http://helix.nih.gov ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] remote user environment variable?
I'm trying to set up a mechanism to copy a local file using a setuid executable, based on whether the registered user has read access to the local file in question. Is there any means for a tool to know the registered user who is running it? David Hoover Helix Systems Staff http://helix.nih.gov ___ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
