[galaxy-dev] remote user environment variable?

2011-01-11 Thread David Hoover
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

[galaxy-dev] phastCons and phastOdds scores

2011-02-01 Thread David Hoover
is looking for. Do I need to install PHAST and generate these score files? 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

Re: [galaxy-dev] histogram tool not working

2011-02-01 Thread David Hoover
I just updated to the most recent version of Galaxy (hg pull -u), and now the error is different: An error occurred running this job: Error in hist.default(list(8, 6, 14, 8, 10, 3, 8, 6, 3, 12, 12, 8, 8, : 'x' must be numeric What gives? David On Feb 1, 2011, at 12:28 PM, David Hoover wrote

Re: [galaxy-dev] histogram tool not working

2011-02-01 Thread David Hoover
R gives the error message 'x' must be numeric, so relevant questions are what version of R do you have, what version or rpy, and what version of Python (since Galaxy's tools tends to invoke R from Python via the ryp library - certainly the histogram tool does). python = 2.6 R = 2.10.0 rpy =

[galaxy-dev] megablast and blastdb

2011-02-15 Thread David Hoover
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

Re: [galaxy-dev] megablast and blastdb

2011-02-16 Thread David Hoover
David Hoover [hoove...@helix.nih.gov] Verzonden: dinsdag 15 februari 2011 22:33 Aan: Galaxy Dev Onderwerp: [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

[galaxy-dev] upload directory of files error

2011-02-17 Thread David Hoover
/library/common/ldda_info.mako.py', line 224 in render_body if job.stdout.strip() != '': AttributeError: 'NoneType' object has no attribute 'strip' Huh? David Hoover Helix Systems Staff http://helix.nih.gov ___ To manage your subscriptions

[galaxy-dev] substitute or replace a value?

2011-02-23 Thread David Hoover
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

[galaxy-dev] samtools mpileup update

2011-08-23 Thread David Hoover
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

Re: [galaxy-dev] prevent downloaded files with .txt added

2011-09-27 Thread David Hoover
. 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

[galaxy-dev] scatterplot broken

2011-10-06 Thread David Hoover
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

Re: [galaxy-dev] scatterplot broken

2011-10-12 Thread David Hoover
) 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

[galaxy-dev] cufflinks version

2011-11-02 Thread David Hoover
What version of cufflinks do the current Galaxy wrappers support? The wiki (http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies) says 1.0.1, but our local instance only works with 1.1.0. Can the wiki be updated? David Hoover Helix Systems Staff http://helix.nih.gov

Re: [galaxy-dev] LDAP authentification

2012-01-19 Thread David Hoover
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

Re: [galaxy-dev] Unix user account/connection and Galaxy connection

2012-01-30 Thread David Hoover
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.

[galaxy-dev] limited tool shed browse

2012-02-22 Thread David Hoover
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

Re: [galaxy-dev] limited tool shed browse

2012-02-28 Thread David Hoover
:02 PM, David Hoover wrote: 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

Re: [galaxy-dev] Error for draw quality score boxplot

2012-03-27 Thread David Hoover
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

Re: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally?

2012-04-27 Thread David Hoover
Not a bad idea. Most of the conversations on this list are very limited and detailed in scope, dealing with the minutia of tools and variables. There isn't much on the bird's eye view. I'm in. On Apr 27, 2012, at 2:45 PM, Ann Black-Ziegelbein wrote: Hi everyone - Here at the University

[galaxy-dev] migrate ownership of galaxy user

2012-06-21 Thread David Hoover
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

[galaxy-dev] configuring job runner for toolshed tools

2012-07-20 Thread David Hoover
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

Re: [galaxy-dev] configuring job runner for toolshed tools

2012-07-23 Thread David Hoover
. 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

Re: [galaxy-dev] configuring job runner for toolshed tools

2012-07-25 Thread David Hoover
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

[galaxy-dev] annoying bug when deleting datasets

2012-07-25 Thread David Hoover
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

[galaxy-dev] fastQC report bug

2012-09-10 Thread David Hoover
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

[galaxy-dev] GATK v2.x

2012-09-11 Thread David Hoover
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

[galaxy-dev] environment variables and paths for toolshed tools

2012-09-12 Thread David Hoover
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 ___ Please keep all replies on the list by using reply all in your

[galaxy-dev] toolshed upload problem

2012-09-12 Thread David Hoover
to the repository that includes the required entry to correct this error. The tool_data_table_conf.xml.sample file already exists within the tarball. Nothing changes if I upload the file separately. Any ideas? David Hoover Helix Systems Staff

[galaxy-dev] where are the tools?

2012-09-25 Thread David Hoover
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

[galaxy-dev] jobName lost when drmaa used with real user use

2012-10-02 Thread David Hoover
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

Re: [galaxy-dev] submitting jobs as the real user

2012-10-03 Thread David Hoover
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

Re: [galaxy-dev] submitting jobs as the real user

2012-10-03 Thread David Hoover
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

[galaxy-dev] trying to set up local toolshed

2012-10-05 Thread David Hoover
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

[galaxy-dev] Fwd: fastQC report bug

2012-10-12 Thread David Hoover
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

[galaxy-dev] picard bug in Add or Replace Groups

2012-10-15 Thread David Hoover
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

[galaxy-dev] determination of errors

2012-10-22 Thread David Hoover
in the .bashrc file, it will automatically write to STDERR, and all jobs, no matter what, are labelled as failing. David Hoover Helix Systems Staff ___ Please keep all replies on the list by using reply all in your mail client. To manage your

[galaxy-dev] no module named gmap

2013-03-06 Thread David Hoover
/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

Re: [galaxy-dev] no module named gmap

2013-03-06 Thread David Hoover
, 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

[galaxy-dev] admin menu column won't scroll

2013-03-06 Thread David Hoover
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

[galaxy-dev] qa_url = slyfox?

2013-08-05 Thread David Hoover
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-dev] browse directories on galaxy server

2013-10-31 Thread David Hoover
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

[galaxy-dev] FTP bug with automatically decompressed files

2013-11-22 Thread David Hoover
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

[galaxy-dev] Library permission page broken

2013-11-27 Thread David Hoover
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.

[galaxy-dev] error with unicode output

2013-12-05 Thread David Hoover
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

Re: [galaxy-dev] error with unicode output

2013-12-05 Thread David Hoover
$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

Re: [galaxy-dev] error with unicode output

2013-12-05 Thread David Hoover
= 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

Re: [galaxy-dev] error with unicode output

2013-12-05 Thread David Hoover
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

Re: [galaxy-dev] error with unicode output

2013-12-06 Thread David Hoover
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

[galaxy-dev] 'Lost connection to MySQL server during query' error

2013-12-13 Thread David Hoover
reloading the URL goes to Galaxy. Is there something different that we need to do now? David Hoover Helix Systems Staff ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions

[galaxy-dev] numpy and scipy

2014-01-21 Thread David Hoover
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

[galaxy-dev] restarting Galaxy without affecting jobs

2014-03-24 Thread David Hoover
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

[galaxy-dev] jobs stuck in new state

2014-03-26 Thread David Hoover
' 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

Re: [galaxy-dev] jobs stuck in new state

2014-03-31 Thread David Hoover
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

Re: [galaxy-dev] problem with bioc_qvalue, Version: 1.34.0

2014-04-17 Thread David Hoover
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

[galaxy-dev] Globus tools for galaxy

2014-05-01 Thread David Hoover
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

[galaxy-dev] display_at_callback

2014-05-02 Thread David Hoover
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

[galaxy-dev] The status is being set to Never installed

2014-08-07 Thread David Hoover
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

[galaxy-dev] tool for STAR RNA-seq aligner

2014-09-24 Thread 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

Re: [galaxy-dev] tool for STAR RNA-seq aligner

2014-09-24 Thread David Hoover
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

Re: [galaxy-dev] tool for STAR RNA-seq aligner

2014-09-25 Thread David Hoover
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

Re: [galaxy-dev] tool for STAR RNA-seq aligner

2014-09-26 Thread David Hoover
. 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

Re: [galaxy-dev] tool for STAR RNA-seq aligner

2014-09-26 Thread David Hoover
does the memory allocation last? David David Hoover, PhD Helix Systems Staff SCB/DCSS/CIT/NIH 301-435-2986 http://helix.nih.gov On Sep 26, 2014, at 9:21 AM, David Hoover hoove...@helix.nih.gov wrote: A colleague of mine mentioned it. I'll ask him where he got his info. Just

[galaxy-dev] datatype directory

2014-09-30 Thread David Hoover
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