Re: [galaxy-dev] Nice 'citable' URLs for Galaxy Tool Shed repositories

2013-02-08 Thread Peter Cock
On Sat, Feb 2, 2013 at 1:56 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Sat, Feb 2, 2013 at 12:46 AM, Greg Von Kuster g...@bx.psu.edu wrote: Hello Peter, I've added an enhanced version of your implementation for citable URLS in the tool shed to change set revision 8720:e27d0dd12752.

Re: [galaxy-dev] Nice 'citable' URLs for Galaxy Tool Shed repositories

2013-02-08 Thread Greg Von Kuster
Hi Peter, On Feb 8, 2013, at 5:26 AM, Peter Cock wrote: On Sat, Feb 2, 2013 at 1:56 PM, Peter Cock p.j.a.c...@googlemail.com wrote: I've noticed one oddity, which is if I go one of the citable URLs like http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira_assembler and then browse away to

Re: [galaxy-dev] Fwd: Desire to contribute

2013-02-08 Thread Paul Boddie
On 06/02/13 20:23, Dave Clements wrote: Please let the list know if any of the ideas posted so far grab you, or if you want further explanation. Thanks for your interest and for picking the Galaxy Project. Efforts like these really help the project move forward. Are there any lists that are

[galaxy-dev] Dependencies on other Tool Shed repositories

2013-02-08 Thread Peter Cock
Hi all, I've been reading http://wiki.galaxyproject.org/ToolShedToolFeatures and focused on the example of EMBOSS where the tool definitions depend on the data type definitions. Here the emboss_5 repository (the tool wrappers) contains depository_dependencies.xml saying: ?xml version=1.0?

Re: [galaxy-dev] [galaxy-user] Why SGE needed for galaxy ?

2013-02-08 Thread Dannon Baker
The workers don't need their own copy of galaxy installed, but a shared filesystem is a requirement for galaxy (in any cluster environment -- see the galaxy wiki for more http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster). Cloudman handles managing NFS for you and sharing the

Re: [galaxy-dev] Fwd: Desire to contribute

2013-02-08 Thread Dannon Baker
On Feb 8, 2013, at 7:03 AM, Paul Boddie paul.bod...@biotek.uio.no wrote: Are there any lists that are more developer-oriented than this one? There seems to be a mixture of end-user problem reports and tool-specific integration discussions on this list, but not so much discussion of framework

Re: [galaxy-dev] Dependencies on other Tool Shed repositories

2013-02-08 Thread Greg Von Kuster
Hi Peter, The changset_revision=xxx tag attribute is a minimum version setting. What this means is that the repository being defined will be installed with any updates to the repository within the set of changeset revisions up to and including the next installable changeset revision for

Re: [galaxy-dev] Fwd: Desire to contribute

2013-02-08 Thread Joachim Jacob |VIB|
The highlight enhancement request on Trello: https://trello.com/c/vUtbTQ7l Since it was imported from Bitbucket, the duplicated card I mentioned refers to the wrong Trello card. Please consider! Thanks, Joachim Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34

Re: [galaxy-dev] Dependencies on other Tool Shed repositories

2013-02-08 Thread Peter Cock
On Feb 8, 2013, at 7:54 AM, Peter Cock wrote: Hi all, I've been reading http://wiki.galaxyproject.org/ToolShedToolFeatures and focused on the example of EMBOSS where the tool definitions depend on the data type definitions. Here the emboss_5 repository (the tool wrappers) contains

[galaxy-dev] Data library not properly showing up

2013-02-08 Thread Joachim Jacob |VIB|
Hi all, The data library I have created is only showing up partially. I have made a data libray, via het Admin menu, with one folder in it. I changed permissions, because I wanted it only to be visible to me. That worked fine. Next I created plenty more folders in that data library. Now,

[galaxy-dev] Deploying LOC files for tool built-in data during a tool installation

2013-02-08 Thread Jean-Frédéric Berthelot
Hi list, The tool I am currently wrapping has built-in data, which may be used by the tool users (through a relevant from_data_table + .LOC file configuration). They are .fasta databases which are rather small and are thus bundled in the tool distribution package. Thanks to the

Re: [galaxy-dev] DustMasker tool for ncbi_blast_plus

2013-02-08 Thread Nicola Soranzo
Il giorno mer, 06/02/2013 alle 20.01 +0100, Nicola Soranzo ha scritto: Hi Peter, I added these file formats mostly as placeholders for a future implementation. Now I have changed a bit the tool by removing acclist and seqloc_xml formats since they are not recognized by the last versions of

[galaxy-dev] Extract genomic DNA job error

2013-02-08 Thread Perez, Ricardo
Hello, I am getting this error when using Extract Genomic DNA (version 2.2.2) empty format: fasta, database: hg19 924 warnings, 1st is: Chromosome by name 'chr22' was not found for build 'hg19'. Skipped 924 invalid lines, 1st is #1, chr22 1625633116287937 NM_001136213 0 -

[galaxy-dev] Error in database after trying the innocently named, but devastatingly evil test in manage_db.sh

2013-02-08 Thread Thon de Boer
Hi, I had a small issue with the total usage of my galaxy system showing some negative random number so I figured my database was a little “off”. I snooped around for some database management tools and found “manage_db.sh” which had an option innocently called “test”. I ran it,

Re: [galaxy-dev] Extract genomic DNA job error

2013-02-08 Thread Jeremy Goecks
Hi Ricardo, This tool requires external data that you'll need to configure. Here's how: (1) download the 2bit file from UCSC for your genomes into a local directory from here: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/ (2) add an entry like this to alignseq.loc (note that you'll

Re: [galaxy-dev] Error in database after trying the innocently named, but devastatingly evil test in manage_db.sh

2013-02-08 Thread Daniel Blankenberg
Hi Thon, The test option runs the upgrade and downgrade of the latest migration script. I'm assuming that you had already run the latest migrations available and the server was up and running OK (other than the dataset size issue) before trying the test command. On a COPY of your database,

Re: [galaxy-dev] [galaxy-user] Why SGE needed for galaxy ?

2013-02-08 Thread Enis Afgan
As far as actually building the image, the recommended method is to use CloudBioLinux build scripts: https://github.com/chapmanb/cloudbiolinux There is a CloudMan flavor of CBL that allows you to build only CloudMan- and Galaxy-required parts:

Re: [galaxy-dev] Error in database after trying the innocently named, but devastatingly evil test in manage_db.sh

2013-02-08 Thread Thon de Boer
Hi Dan, I tried that but it failed ofcourse since the table it tries to drop from 109 - 108 does not exisit. sh manage_db.sh downgrade 108 109 - 108... 0109_add_repository_dependency_tables DEBUG 2013-02-08 13:04:33,464 Dropping repository_repository_dependency_association table

Re: [galaxy-dev] Error in database after trying the innocently named, but devastatingly evil test in manage_db.sh

2013-02-08 Thread Thon de Boer
OK..I tried it a few more times and this time with different results! HA! I knew I wasn’t insane…As long as you try anything often enough in the same manner, you WILL get a different outcome…Yea uncertainty principle! I also had to resort to downloading the whole complete galaxy-dist from

[galaxy-dev] Galaxy February 8, 2013 Distribution News Brief

2013-02-08 Thread Jennifer Jackson
Galaxy Feb 8, 2013 Distribution News Brief http://wiki.galaxyproject.org/News/2013_02_08_GalaxyNewsBrief *Complete News Brief http://wiki.galaxyproject.org/DevNewsBriefs/2013_02_08 * *Highlights:* * /Improvements/ to our release process