Re: [galaxy-dev] Workflow steps collapsible to just title bar

2011-01-31 Thread Peter Cock
On Mon, Jan 31, 2011 at 5:59 PM, Dannon Baker dannonba...@me.com wrote: On Jan 31, 2011, at 11:34 AM, Peter Cock wrote: I may have found a bug though - I have several workflows using my SignalP wrapper, which has a select parameter for model type. This has been marked as to be set at runtime

Re: [galaxy-dev] Problem upgrading DB from 72 to 73 (SQLite)

2011-02-02 Thread Peter Cock
On Wed, Feb 2, 2011 at 1:27 PM, Peter Cock p.j.a.c...@googlemail.com wrote: Should I file a bug report? $ sh manage_db.sh upgrade 72 - 73... Migration script to add 'ldda_parent_id' column to the implicitly_converted_dataset_association table. Adding ldda_parent_id column

Re: [galaxy-dev] Problem upgrading DB from 72 to 73 (SQLite)

2011-02-02 Thread Peter Cock
On Wed, Feb 2, 2011 at 5:39 PM, Kanwei Li kan...@gmail.com wrote: This happens with a lot of the migration scripts... I think as long as you have the new column (I just checked, mine does) it should be fine. OK, so its basically a harmless warning - I'll ignore it then. Thanks. Peter

Re: [galaxy-dev] Version Error and Python 2.7

2011-02-02 Thread Peter Cock
On Wed, Feb 2, 2011 at 6:02 PM, John David Osborne ozb...@uab.edu wrote: I have (or rather had) a functional galaxy installation on a CentOS box running python 2.4. I did an mecurial update for the first time and broke my installation. It looks like some eggs are getting out of date and when I

[galaxy-dev] Barcode/adapter/primer trimming/filtering of sequences/reads

2011-02-03 Thread Peter Cock
Hi all, I'm currently working with some 454 data where the sample was amplified with selective primers, and therefore the reads need a little processing to remove the primer sequences before assembly or mapping (something that sff_extract cleverly spots and warns the user about when doing an SFF

Re: [galaxy-dev] Barcode/adapter/primer trimming/filtering of sequences/reads

2011-02-03 Thread Peter Cock
On Thu, Feb 3, 2011 at 11:54 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi all, I'm currently working with some 454 data where the sample was amplified with selective primers, and therefore the reads need a little processing to remove the primer sequences before assembly or mapping

Re: [galaxy-dev] Barcode/adapter/primer trimming/filtering of sequences/reads

2011-02-08 Thread Peter Cock
On Tue, Feb 8, 2011 at 8:15 AM, Kevin Lam abou...@gmail.com wrote: Have you looked at http://code.google.com/p/cutadapt/ Features Gapped alignment with mismatches and indels, that is, errors in the adapter are tolerated Finds adapters both in the 5' and 3' ends of reads Accepts FASTQ,

[galaxy-dev] Hiding a tool via tool_conf.xml

2011-02-10 Thread Peter Cock
Hi all, I'm aware that in an individual tool's XML wrapper you can add hidden=true to the tool element to hide the tool from the listing shown in Galaxy's left hand panel (but the tool is still loaded and can be called by old workflows etc). Can this be done via the tool_conf.xml file as well?

Re: [galaxy-dev] unable to login user to local instance

2011-02-18 Thread Peter Cock
On Fri, Feb 18, 2011 at 5:01 PM, Ryan Golhar golha...@umdnj.edu wrote: Ok, I don't know what happened with this...I reinstalled from scratch and ... Traceback (most recent call last):  File /home/galaxy/galaxy-dist/tools/new_operations/get_flanks.py, line 16, in ? ...  File

[galaxy-dev] Problem upgrading DB from 73 to 75 (on SQLite)

2011-02-21 Thread Peter Cock
Hi all, I've just updated my Mac development machine with the latest galaxy-central, and run.sh tells me the database needs to be updated from 73 to 75. Note this is running on SQLite. Running manage_db.sh upgrade gives an ImportError: No module named migrate.versioning.shell I just grabbed a

Re: [galaxy-dev] Hiding a tool via tool_conf.xml

2011-03-02 Thread Peter Cock
On Thu, Feb 10, 2011 at 5:58 PM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi all, I'm aware that in an individual tool's XML wrapper you can add hidden=true to the tool element to hide the tool from the listing shown in Galaxy's left hand panel (but the tool is still loaded and can

[galaxy-dev] Shared a value for multiple set-at-runtime workflow parameters

2011-03-02 Thread Peter Cock
Hi all, I have a multi-step workflow where I've marked some parameters to be set at run time (in this case, a minimum read length, used in two different workflow steps). I want to use the same parameter value in multiple tools, rather than give the user one prompt for each tool. Is this possible?

Re: [galaxy-dev] Shared a value for multiple set-at-runtime workflow parameters

2011-03-02 Thread Peter Cock
On Wed, Mar 2, 2011 at 2:51 PM, Dannon Baker dannonba...@me.com wrote: Peter- Just a quick response to your first question-  you might want to give the workflow parameters feature a shot to see if it does what you're looking to do.  Within the workflow editor, instead of setting a value to

Re: [galaxy-dev] Shared a value for multiple set-at-runtime workflow parameters

2011-03-02 Thread Peter Cock
On Wed, Mar 2, 2011 at 3:21 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Wed, Mar 2, 2011 at 2:51 PM, Dannon Baker dannonba...@me.com wrote: Peter- Just a quick response to your first question-  you might want to give the workflow parameters feature a shot to see if it does what you're

Re: [galaxy-dev] Shared a value for multiple set-at-runtime workflow parameters

2011-03-02 Thread Peter Cock
On Wed, Mar 2, 2011 at 3:42 PM, Peter Cock p.j.a.c...@googlemail.com wrote: P.S. I do like the color highlighting and live substitution of the workflow parameters into each tool step that uses them. Very slick! That was the good news. Now the bad news - two bug reports. Firstly if you clear

[galaxy-dev] QUAL file format(s)

2011-03-03 Thread Peter Cock
Hi all, Is there any documentation on what Galaxy means by the different qual formats? In particular why is there a qual454 and not a qualsanger (to match fastq)? Historically QUAL files were used back in Sanger/capillary sequencing by PHRED, and just hold PHRED scores as integers. This was

[galaxy-dev] Fwd: [Bosc] Bioinformatics Open Source Conference (BOSC 2011)--Call for Abstracts

2011-03-03 Thread Peter Cock
: Nomi Harris and Peter Rice (co-chairs); Brad Chapman, Peter Cock, Erwin Frise, Darin London, Ron Taylor ___ BOSC mailing list b...@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bosc

Re: [galaxy-dev] missing setup.sh in galaxy source code

2011-03-06 Thread Peter Cock
On Sun, Mar 6, 2011 at 6:36 AM, Zhi-Wei Lu z...@ucdavis.edu wrote: Hi Galaxy developers, I have download the galaxy code via mercurial hg clone https://bitbucket.org/galaxy/galaxy-central The downloaded code, however, does not contain the setup.sh file. Could you let me know how do I run

Re: [galaxy-dev] possible bug - user log in / browser cache

2011-03-07 Thread Peter Cock
On Mon, Mar 7, 2011 at 5:56 PM, Nate Coraor n...@bx.psu.edu wrote: Ryan Golhar wrote: I have a local instance running.  When I'm logged in as user1, log out, then try to log in as user2, I keep getting the You have been logged out message. Its as if the browser's cache is retaining some

Re: [galaxy-dev] Info button

2011-03-09 Thread Peter Cock
On Wed, Mar 9, 2011 at 10:19 AM, SHAUN WEBB swe...@staffmail.ed.ac.uk wrote: Hi, I really like the new feature to show dataset information and parameters used to run the tool. Problem is that the link doesn't always work. It seems as though the first time I open a history and click the i the

Re: [galaxy-dev] Info button

2011-03-09 Thread Peter Cock
On Wed, Mar 9, 2011 at 10:52 AM, Brad Chapman chapm...@50mail.com wrote: Shaun and Peter; Hi, I really like the new feature to show dataset information and parameters used to run the tool. Problem is that the link doesn't always work. It seems as though the first time I open a

[galaxy-dev] Creating Roles and groups

2011-03-10 Thread Peter Cock
Hi all, I've had a little play with our local Galaxy to try and get a feel for libraries, groups and roles. I see when you create a new role (e.g. Project X), you have a tick box to create a group of the same name. However, when you create a new group, these is no such tick box to create a role

[galaxy-dev] Upload files from filesystem paths - backwards checkboxes

2011-03-10 Thread Peter Cock
Hi all, Via the Galaxy admin interface, I'm currently importing some BAM files into a library from the local file system. Since they are big, I don't want Galaxy to copy them. So I looked at the Copy data into Galaxy? option and made sure it wasn't ticked. Galaxy did copy the file :( I looked

[galaxy-dev] Error importing BAM file into Library

2011-03-10 Thread Peter Cock
Hi all, I think I have fallen over the same problem Glen Beane reported in Nov 2010, http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-November/003943.html I recall from reading the mailing list, that when you import a BAM file into Galaxy, it gets sorted and indexed. That makes sense since most

Re: [galaxy-dev] Problem upgrading DB from 73 to 75 (on SQLite)

2011-03-11 Thread Peter Cock
On Mon, Feb 21, 2011 at 3:41 PM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi all, I've just updated my Mac development machine with the latest galaxy-central, and run.sh tells me the database needs to be updated from 73 to 75. Note this is running on SQLite. Running manage_db.sh upgrade

Re: [galaxy-dev] Upload files from filesystem paths - backwards checkboxes

2011-03-11 Thread Peter Cock
On Thu, Mar 10, 2011 at 5:53 PM, Glen Beane glen.be...@jax.org wrote: On Mar 10, 2011, at 12:24 PM, Peter Cock wrote: Hi all, Via the Galaxy admin interface, I'm currently importing some BAM files into a library from the local file system. Since they are big, I don't want Galaxy to copy

Re: [galaxy-dev] Upload files from filesystem paths - backwards checkboxes

2011-03-11 Thread Peter Cock
On Fri, Mar 11, 2011 at 3:04 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hello Peter, Thanks for the patch - I've applied a corrected version of it in change set 5215:74c4dd43485a.  Let  me know if you'd rather have me flip the Copy data into Galaxy? feature.  I'd be happy to, but I don't

Re: [galaxy-dev] Problem upgrading DB from 73 to 75 (on SQLite)

2011-03-17 Thread Peter Cock
On Thu, Mar 17, 2011 at 7:47 PM, Nate Coraor n...@bx.psu.edu wrote: Peter Cock wrote: $ python -ES ./scripts/fetch_eggs.py Fetched http://eggs.g2.bx.psu.edu/Mako/Mako-0.2.5-py2.6.egg ... Fetched http://eggs.g2.bx.psu.edu/PasteScript/PasteScript-1.7.3-py2.6.egg Were there really no eggs

Re: [galaxy-dev] Error importing BAM file into Library

2011-03-18 Thread Peter Cock
Greg wrote: Breaking this issue into the following 2 parts, here is the status. 1. Don't alter the contents of files being uploaded to a data library if using the upload_directory or upload_paths options in conjunction with the Link to files without copying into Galaxy option. This

[galaxy-dev] History information popup broken on library entries?

2011-03-18 Thread Peter Cock
Hi all, I've been exploring how to use Galaxy's shared library functionality, and have noticed that once imported into a working history, that the little 'i' information icon's black popup window isn't working for these datasets. All it says is 'Could not find the job for this dataset.' This

Re: [galaxy-dev] Metadata recursion error with empty tabular file (with patch)

2011-03-18 Thread Peter Cock
On Fri, Mar 18, 2011 at 6:12 PM, Kanwei Li kan...@gmail.com wrote: Thanks for reporting, committed fix https://bitbucket.org/galaxy/galaxy-central/changeset/3070455afbdd Thanks, Peter ___ Please keep all replies on the list by using

Re: [galaxy-dev] Error importing BAM file into Library

2011-03-23 Thread Peter Cock
On Wed, Mar 23, 2011 at 4:24 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hello Peter, On Mar 18, 2011, at 11:26 AM, Peter Cock wrote: Having checked my BAM files with samtools, I can confirm they don't have the SO header. samtools view -H myfile.bam | grep SO: They were generated with BWA

[galaxy-dev] Using wget/curl with Tool Shed?

2011-03-28 Thread Peter Cock
Hi all, I'm trying to download and install something from the Galaxy Tool Shed http://community.g2.bx.psu.edu/ on to our sever. To do this, I'd like to copy/paste the URL of a tool's tar ball (or individual XML file etc) from my browser running on my desktop to a terminal window logged in to our

Re: [galaxy-dev] Alternative bowtie tools

2011-03-29 Thread Peter Cock
On Tue, Mar 29, 2011 at 1:31 AM, Assaf Gordon gor...@cshl.edu wrote: Hello all, We're developing alternative bowtie tools that more closely suit our needs, are we're happy to share (and get comments). The main differences are: 1. separate tools for paired-end and single-end Sounds sensible

Re: [galaxy-dev] Alternative bowtie tools

2011-03-29 Thread Peter Cock
On Tue, Mar 29, 2011 at 4:46 PM, Assaf Gordon gor...@cshl.edu wrote: Hi Dan, Daniel Blankenberg wrote, On 03/29/2011 10:55 AM: When files are added to Galaxy, the datatype can be directly set to any of the fastq variants (e.g. fastqillumina), which removes the requirement of grooming (but

[galaxy-dev] Default value for data_column not working?

2011-03-30 Thread Peter Cock
Hi all, I'm trying to write a new tool working with tabular data (specifically a Reciprocal Best Hits (RBH) tool using BLAST style tabular output). I want the user to be able to choose a column number (from one of the input files), but I have a default column in mind. However, Galaxy doesn't

[galaxy-dev] Updating BLAST+ wrapper

2011-03-31 Thread Peter Cock
Hi all, The NCBI have just released BLAST 2.2.25+ which includes some interesting new stuff of interest to the tabular output, i.e. Added support for query and subject length to tabular output I would therefore like to update my BLAST+ wrappers in Galaxy to add these two columns to the

Re: [galaxy-dev] Default value for data_column not working?

2011-04-01 Thread Peter Cock
On Fri, Apr 1, 2011 at 3:55 PM, Kanwei Li kan...@gmail.com wrote: Hi Peter, I don't see your attempt to use default in the example given. A bit more detail? -K Hi Kanwei, My example tool is now here: https://bitbucket.org/peterjc/galaxy-central/changeset/198bf927ca30 As per the original

Re: [galaxy-dev] Updating BLAST+ wrapper

2011-04-04 Thread Peter Cock
On Fri, Apr 1, 2011 at 12:01 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Thu, Mar 31, 2011 at 6:28 PM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi all, The NCBI have just released BLAST 2.2.25+ which includes some interesting new stuff of interest to the tabular output, ... One

Re: [galaxy-dev] Updating BLAST+ wrapper

2011-04-04 Thread Peter Cock
On Mon, Apr 4, 2011 at 12:19 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Fri, Apr 1, 2011 at 12:01 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Thu, Mar 31, 2011 at 6:28 PM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi all, The NCBI have just released BLAST 2.2.25+ which

Re: [galaxy-dev] Updating BLAST+ wrapper

2011-04-04 Thread Peter Cock
On Mon, Apr 4, 2011 at 3:07 PM, Kanwei Li kan...@gmail.com wrote: Hi Peter, I think you need to merge your commits as I cannot seem to transplant or import the patches properly. K Hi Kanwei, I'm not sure why they won't transplant - they are both on this fresh branch from the trunk, with

Re: [galaxy-dev] Updating BLAST+ wrapper

2011-04-04 Thread Peter Cock
On Mon, Apr 4, 2011 at 4:03 PM, Kanwei Li kan...@gmail.com wrote: I tried both ways, no dice (you can try yourself with a clean galaxy-central base) I'm a bit puzzled and not an hg expert. Was there an error message? And for plan (B), what went wrong with using patch and the raw changes?

Re: [galaxy-dev] Updating BLAST+ wrapper

2011-04-04 Thread Peter Cock
On Mon, Apr 4, 2011 at 4:36 PM, Kanwei Li kan...@gmail.com wrote: dhcp243253:galaxy-central kanwei$ hg transplant -s ~/peter/galaxy-central/ -b blast25 searching for changes changeset:   5585:ab40f95393ec branch:      blast25 parent:      5583:086c9c2c52b9 user:        peterjc

Re: [galaxy-dev] Updating BLAST+ wrapper

2011-04-04 Thread Peter Cock
On Mon, Apr 4, 2011 at 5:55 PM, Kanwei Li kan...@gmail.com wrote: Done the manual way Thanks. I was hoping to have finished this today, but it turns out there are some subtle but annoying changes to how BLAST records the hit id/name/description in their XML file which make the script to

[galaxy-dev] Ignoring white space differences in test output

2011-04-05 Thread Peter Cock
Hi all, I'd like to write a tool test where the sample output and the generated output are the same except for white space. i.e. running diff with the -w switch reports no differences. Is this possible at the moment with the Galaxy test framework? I'm hoping for a test output attribute. I don't

Re: [galaxy-dev] Ignoring white space differences in test output

2011-04-05 Thread Peter Cock
On Tue, Apr 5, 2011 at 10:58 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi all, I'd like to write a tool test where the sample output and the generated output are the same except for white space. i.e. running diff with the -w switch reports no differences. Is this possible

Re: [galaxy-dev] Updating BLAST+ wrapper

2011-04-05 Thread Peter Cock
On Mon, Apr 4, 2011 at 6:07 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Mon, Apr 4, 2011 at 5:55 PM, Kanwei Li kan...@gmail.com wrote: Done the manual way Thanks. I was hoping to have finished this today, but it turns out there are some subtle but annoying changes to how BLAST

[galaxy-dev] Ratings on Tool Shed broken?

2011-04-05 Thread Peter Cock
Hi all, I had wondered why none of the tools on the Galaxy Tool Shed had a rating, and had assumed it was just that so far no-one had bothered. I have a new theory, it doesn't work? I just viewed Brad's BAM to BigWig tool, clicked on Tool Actions then Rate Tool, and got: Server Error An error

Re: [galaxy-dev] SGE and Galaxy (a different approach)

2011-04-05 Thread Peter Cock
On Tue, Apr 5, 2011 at 5:27 PM, andrew stewart andrew.c.stew...@gmail.com wrote: I'm aware of how to configure Galaxy to use SGE in universe_wsgi.ini, however what I want to do is a little different.  Because I only want certain processes to be submitted to the queue, I'd rather control this at

Re: [galaxy-dev] Relative file path in Galaxy

2011-04-06 Thread Peter Cock
On Wed, Apr 6, 2011 at 12:44 AM, Zhe Chen z...@lanl.gov wrote: Hi, My tool has a script reads a file in the same directory as the script. When I try to use relative path to read the file, it works by directly run it, but does not work when calling from Galaxy. Absolute path will work, but I

Re: [galaxy-dev] another update problem

2011-04-11 Thread Peter Cock
On Mon, Apr 11, 2011 at 7:26 PM, Ryan Golhar golha...@umdnj.edu wrote: I just updated my local galaxy instance using hg pull, and the history items are no longer expandable.  What happened? Which browser(s) are affected? I recall reporting some issues with Internet Explorer only and the history

Re: [galaxy-dev] Getting tool dirpath in a Python code file

2011-04-14 Thread Peter Cock
On Thu, Apr 14, 2011 at 2:08 PM, Leandro Hermida soft...@leandrohermida.com wrote: Hi, I have a tool with a code file=my_script.py/ tag and in that code file I'm trying to get the tool dirpath where that script and the tool XML exist.  I've tried:

[galaxy-dev] NLStradamus wrapper (for nuclear localization signals)

2011-04-14 Thread Peter Cock
Hi all, I just wanted to mention (to avoid duplicate work) that I have a working Galaxy wrapper for NLStradamus v1.6, a tool for prediction of nuclear localization signals (NLSs) from a protein FASTA file. The wrapper does a little reformatting of the output to get a clean tabular file for use in

Re: [galaxy-dev] Getting tool dirpath in a Python code file

2011-04-15 Thread Peter Cock
On Thu, Apr 14, 2011 at 2:56 PM, Leandro Hermida soft...@leandrohermida.com wrote: On Thu, Apr 14, 2011 at 3:17 PM, Peter Cock p.j.a.c...@googlemail.com wrote: For standard Python tools in Galaxy, I'm using os.path.split(sys.argv[0])[0] to get the path, which on reflection probably should

[galaxy-dev] Setting min/max limit on repeat tag in tool XML file

2011-04-19 Thread Peter Cock
Hi all, I'm working on a tool where the repeat tag looks like an elegant solution - however I want to limit the number of repeats to be 1, 2 or 3. i.e. I want to set min=1 and max=3 attributes for the repeat, based on analogy to the param tag. Is this possible, but not documented here?

Re: [galaxy-dev] Setting min/max limit on repeat tag in tool XML file

2011-04-19 Thread Peter Cock
On Tue, Apr 19, 2011 at 1:46 PM, Daniel Blankenberg d...@bx.psu.edu wrote: Hi Peter, Yes, setting min and max values in the repeat tag should work as you need. As you point out, it is probably not well documented, so please let us know if it isn't working as you imagine it should. Thanks

Re: [galaxy-dev] Setting min/max limit on repeat tag in tool XML file

2011-04-19 Thread Peter Cock
On Tue, Apr 19, 2011 at 2:23 PM, Peter Cock p.j.a.c...@googlemail.com wrote: What I need to work out now is how to use repeat parameters in the unit tests. There seems to be examples in tools/mutation/visualize.xml and tools/plotting/xy_plot.xml which only use the first repeat... I've tried

Re: [galaxy-dev] Setting min/max limit on repeat tag in tool XML file

2011-04-19 Thread Peter Cock
On Tue, Apr 19, 2011 at 3:38 PM, Daniel Blankenberg d...@bx.psu.edu wrote: Hi Peter, The test framework could use a bit of work, and better handling of grouping-style parameters (such as repeats) is one significant area needing improvement. Noted. Is there an issue open on this already?

[galaxy-dev] BLAST+ HTML output broken

2011-04-19 Thread Peter Cock
Hi Kanwei, I noticed that the BLAST+ output options for HTML are not working, a side effect of my recent refactoring. Could you transplant/merge this fix and test please: https://bitbucket.org/peterjc/galaxy-central/changeset/e1e6f92e07bf

[galaxy-dev] Plotting tools - best output format? PDF, PNG, ...

2011-04-20 Thread Peter Cock
Hi all, I'm working on a simple plotting tool, and currently I am using PDF output since this is vector based (so it can be rescaled without loss of quality) and can be edited easily enough for use in publications. However, at least on my OS/Browser, Galaxy does not show the PDF files in situ,

Re: [galaxy-dev] Plotting tools - best output format? PDF, PNG, ...

2011-04-20 Thread Peter Cock
On Wed, Apr 20, 2011 at 10:07 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi all, I'm working on a simple plotting tool, and currently I am using PDF output since this is vector based (so it can be rescaled without loss of quality) and can be edited easily enough for use in publications

Re: [galaxy-dev] Plotting tools - best output format? PDF, PNG, ... SVG!

2011-04-20 Thread Peter Cock
On Wed, Apr 20, 2011 at 4:30 PM, Pieter Neerincx pieter.neeri...@gmail.com wrote: Hi Peter, On Apr 20, 2011, at 11:07 AM, Peter Cock wrote: Hi all, ...cut... How about SVG? Don't most of the mainline browsers have reasonably good SVG support built in (possibly via a plugin)? Yep, SVG

Re: [galaxy-dev] Plotting tools - best output format? PDF, PNG, ... SVG!

2011-04-21 Thread Peter Cock
On Thu, Apr 21, 2011 at 10:50 AM, Pieter Neerincx pieter.neeri...@gmail.com wrote: Hi Peter, On Apr 20, 2011, at 5:47 PM, Peter Cock wrote: On Wed, Apr 20, 2011 at 4:30 PM, Pieter Neerincx pieter.neeri...@gmail.com wrote: Hi Peter, On Apr 20, 2011, at 11:07 AM, Peter Cock wrote: Hi all

[galaxy-dev] Galaxy tools' priority level (nice)

2011-04-21 Thread Peter Cock
Hi all, Our Galaxy is running on a shared server which will sometimes be running other computationally demanding jobs (outside of Galaxy). In some cases I'd like these to have priority, perhaps by having Galaxy run the tool child processes at a nice level of 10 (say). Is there any built in way

Re: [galaxy-dev] Galaxy tools' priority level (nice)

2011-04-21 Thread Peter Cock
On Thu, Apr 21, 2011 at 5:43 PM, Assaf Gordon gor...@cshl.edu wrote: Hi Peter, Peter Cock wrote, On 04/21/2011 11:00 AM: Is there any built in way to control the Unix priority level (e.g. nice or ionice) used to run tasks? I don't see anything on here, but perhaps I'm looking in the wrong

Re: [galaxy-dev] Galaxy tools' priority level (nice)

2011-04-22 Thread Peter Cock
On Thu, Apr 21, 2011 at 9:27 PM, Assaf Gordon gor...@cshl.edu wrote: Peter Cock wrote, On 04/21/2011 12:59 PM: On Thu, Apr 21, 2011 at 5:43 PM, Assaf Gordon gor...@cshl.edu wrote: I know nice isn't perfect, but in the case of the sys admin setting up Galaxy, we don't have the human laziness

Re: [galaxy-dev] NLStradamus wrapper (for nuclear localization signals)

2011-04-22 Thread Peter Cock
On Thu, Apr 14, 2011 at 5:38 PM, Peter Cock wrote: Hi all, I just wanted to mention (to avoid duplicate work) that I have a working Galaxy wrapper for NLStradamus v1.6, a tool for prediction of nuclear localization signals (NLSs) from a protein FASTA file. The wrapper does a little

Re: [galaxy-dev] Could anyone body tell me why our C program do not work in galaxy

2011-04-22 Thread Peter Cock
2011/4/22 liyanhui607 liyanhui...@163.com: Dear Sir,   We have a program writen in C lanuage. It can run nomally in linux environment.    We plan to add it to galaxy, but it did not work.    The C file after complie named shortest-path The

Re: [galaxy-dev] Could anyone body tell me why our C program do not work in galaxy

2011-04-25 Thread Peter Cock
2011/4/25 liyanhui607 liyanhui...@163.com: Thank you  very much! After I have added it to the path, it can work now. Best Wishes! Yan-Hui Li Oh good. Peter P.S. Please keep the mailing list on replies. ___ Please keep all replies on

[galaxy-dev] Staged Method for cluster running SGE?

2011-04-26 Thread Peter Cock
Hi all, So far we've been running our local Galaxy instance on a single machine, but I would like to be able to offload (some) jobs onto our local SGE cluster. I've been reading https://bitbucket.org/galaxy/galaxy-central/wiki/Config/Cluster Unfortunately in our setup the SGE cluster head node

Re: [galaxy-dev] Staged Method for cluster running SGE?

2011-04-26 Thread Peter Cock
On Tue, Apr 26, 2011 at 12:10 PM, Sean Davis sdav...@mail.nih.gov wrote: On Tue, Apr 26, 2011 at 5:11 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi all, So far we've been running our local Galaxy instance on a single machine, but I would like to be able to offload (some) jobs onto our

[galaxy-dev] Basic HTML markup in loc files (e.g. italics in descriptions)

2011-05-03 Thread Peter Cock
Hi all, In biology we often want to use italics, the key examples that come to mind are species and gene names. I think it is natural therefore to want to be able to use italics in the description of data resources in Galaxy's loc files. For example, in our local Galaxy for the BLAST databases

[galaxy-dev] Reciprocal Best Hits (RBH) from BLAST tabular output

2011-05-04 Thread Peter Cock
Hi all, I mentioned just over a month ago that I had written a Galaxy tool to do find Reciprocal Best Hits (RBH) from BLAST tabular output or similar (e.g. Bill Pearson's FASTA tabular output). http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-March/004799.html

Re: [galaxy-dev] quick question: how can i supply the user's email address to a tool?

2011-05-06 Thread Peter Cock
On Fri, May 6, 2011 at 8:18 AM, Hans-Rudolf Hotz h...@fmi.ch wrote: Hi Ed You can use the variable $userEmail in the 'command' tag of the tool definition file Regards, Hans That should probably be listed on the wiki, https://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax Are

Re: [galaxy-dev] options from file

2011-05-06 Thread Peter Cock
On Fri, May 6, 2011 at 10:17 AM, SHAUN WEBB swe...@staffmail.ed.ac.uk wrote: Hi, I have created a tool that will fetch sequences for selected IDs from a tabular file containing multiple IDs and additional info. I want the tool config to scan the first column of the tab file for IDs and

Re: [galaxy-dev] adding to the wiki

2011-05-07 Thread Peter Cock
On Sat, May 7, 2011 at 11:51 AM, Frederick van Staden cmptrwiz...@gmail.com wrote: Is there a way i can contribute to the wiki? Regards Fred Register an account on bitbucket, and you should be able to edit it. Peter ___ Please keep all

Re: [galaxy-dev] [galaxy-user] Megblast GIs

2011-05-07 Thread Peter Cock
On Sat, May 7, 2011 at 12:01 AM, Douglas Rhoads drho...@uark.edu wrote: We have a local install of Galaxy and are using it for training grad and undergrad students (using the Windshield Splatter data).  We have a relatively new install and the Megablast seems to be doing something funny with

Re: [galaxy-dev] Megablast GIs

2011-05-07 Thread Peter Cock
On Saturday, May 7, 2011, drho...@uark.edu wrote: Thanks Peter,  I debated which to post to. This is just using the Megablast tool in Galaxy.  My IT people are not Biologists.  They had this working fine and some tweak has screwed up the GI column in the results file.  It should be the

[galaxy-dev] Galaxy administrators - admin_users setting

2011-05-09 Thread Peter Cock
Hi all, To make someone an administrator on a local Galaxy install, do I just need to add their email (login) to the comma separated setting admin_users in universe_wsgi.ini? https://bitbucket.org/galaxy/galaxy-central/wiki/Admin/AdminInterface I have this working on one server, but it doesn't

Re: [galaxy-dev] Galaxy administrators - admin_users setting

2011-05-09 Thread Peter Cock
On Mon, May 9, 2011 at 12:48 PM, Hans-Rudolf Hotz h...@fmi.ch wrote: Hi Peter First,the obvious question: Have you restarted galaxy? Yes, and I tried hard reloads in two different browsers (both of which are working on the primary server). Second: I vaguely remember a similar problem, and if

Re: [galaxy-dev] Galaxy administrators - admin_users setting

2011-05-09 Thread Peter Cock
On Mon, May 9, 2011 at 1:59 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Mon, May 9, 2011 at 12:48 PM, Hans-Rudolf Hotz h...@fmi.ch wrote: Hi Peter First,the obvious question: Have you restarted galaxy? Yes, and I tried hard reloads in two different browsers (both of which are working

[galaxy-dev] Wrappers for NCBI BLAST+ blastdbcmd

2011-05-09 Thread Peter Cock
Hi all, I've done a couple of wrappers for the NCBI BLAST+ tool blastdbcmd. The NCBI BLAST+ tool blastdbcmd replaces the NCBI legacy BLAST tool fastacmd. The wrapper first lets you get a FASTA file of sequences from a database by their ID (which works best if your database was built with

Re: [galaxy-dev] Filter data on any column and missing values

2011-05-12 Thread Peter Cock
On Thu, Apr 7, 2011 at 7:00 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Thu, Apr 7, 2011 at 4:28 PM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi all, I have just found a problem using the Filter data on any column using simple expressions tool, i.e. files tools/stats/filters.xml

Re: [galaxy-dev] param type=float optional=true doesn't work

2011-05-12 Thread Peter Cock
On Thu, May 12, 2011 at 6:03 PM, Leandro Hermida wrote: Hi, how do you make float parameter types fully optional? optional=true doesn't work. -Leandro Sadly this is a known bug I reported some time ago: https://bitbucket.org/galaxy/galaxy-central/issue/403 Peter

Re: [galaxy-dev] Reload .loc files without restarting Galaxy system?

2011-05-13 Thread Peter Cock
On Wed, Apr 6, 2011 at 10:30 PM, Luobin Yang yangl...@isu.edu wrote: Hi, The reload a tool's configuration menu avoids restarting Galaxy system when a tool's web interface changed, but it doesn't seem to reload the .loc files that a tool's XML file uses. I am wondering if it's possible to

Re: [galaxy-dev] Wrapper generator.

2011-05-13 Thread Peter Cock
On Fri, May 13, 2011 at 2:12 PM, J. F. J. Laros j.f.j.la...@lumc.nl wrote: Hi Pieter, Thanks for the reply, but from the looks of it, this is a way to incorporate webservice clients into galaxy. What I want is slightly different. I'm talking about adding a normal command line tool (an

Re: [galaxy-dev] A tool with no inputs

2011-05-16 Thread Peter Cock
On Mon, May 16, 2011 at 4:53 PM, Duddy, John jdu...@illumina.com wrote: Doesn’t this violate one of the basic tenets of Galaxy – reproducibility? Without the ability to provide full traceability to the inputs, one can make no guarantees about the outputs. Yes, but not everyone puts that as a

Re: [galaxy-dev] Reciprocal Best Hits (RBH) from BLAST tabular output

2011-05-17 Thread Peter Cock
On Wed, May 4, 2011 at 9:59 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi all, I mentioned just over a month ago that I had written a Galaxy tool to do find Reciprocal Best Hits (RBH) from BLAST tabular output or similar (e.g. Bill Pearson's FASTA tabular output). http

Re: [galaxy-dev] User list and disk space?

2011-05-17 Thread Peter Cock
On May 16, 2011, at 10:18 AM, Louise-Amelie Schmitt wrote: Hello I would like to add a column in the admin panel's user list with the sum of the file size of every dataset in each user's histories that don't belong to any ibrary. Is there a way to do that? On Mon, May 16, 2011 at 7:18

[galaxy-dev] Select first/last N rows from grouped tabular files (e.g. top BLAST hits)

2011-05-17 Thread Peter Cock
Hi all, I'm wondering if the following task can be done in Galaxy with the standard tools. The specific example is selecting the top (e.g. 3) match sequences for each blast query, but I see this problem as much more general than a Select top BLAST hits tool. I want to select the first few (e.g.

[galaxy-dev] Published Workflows menu location

2011-05-18 Thread Peter Cock
Hi all, I recently started trying out the Share workflow functionality on our local Galaxy, so that I could make available some general interest workflows to all our users, rather than sharing them with individuals one by one. However, once published, it was not easy to find them! I eventually

Re: [galaxy-dev] Reciprocal Best Hits (RBH) from BLAST tabular output

2011-05-18 Thread Peter Cock
On Wed, May 18, 2011 at 3:54 AM, Kanwei Li kan...@gmail.com wrote: Hi Peter, I think the tool shed would be appropriate for this... -K OK - I'll do that. Thanks, Peter ___ Please keep all replies on the list by using reply all in your

Re: [galaxy-dev] Select first/last N rows from grouped tabular files (e.g. top BLAST hits)

2011-05-18 Thread Peter Cock
On Tue, May 17, 2011 at 5:30 PM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi all, I'm wondering if the following task can be done in Galaxy with the standard tools. The specific example is selecting the top (e.g. 3) match sequences for each blast query, but I see this problem as much more

Re: [galaxy-dev] Select first/last N rows from grouped tabular files (e.g. top BLAST hits)

2011-05-19 Thread Peter Cock
On Thu, May 19, 2011 at 7:33 PM, madduri gal...@ci.uchicago.edu wrote: I wonder if somebody can give me more context around this issue.. On 3rd May I emailed IBX about their Galaxy install and one of the (in house) tools mentioned on the workflow image here:

Re: [galaxy-dev] Tools: dynamic check of file type?

2011-05-20 Thread Peter Cock
2011/5/20 Louise-Amélie Schmitt louise-amelie.schm...@embl.de: Hello Is there a way to check the file type with a conditional tag set within a tool? For example, if the tool can accept several file types but I have to make cheetah shut off some stuff for a couple of them? You can do

Re: [galaxy-dev] Tools: dynamic check of file type?

2011-05-20 Thread Peter Cock
2011/5/20 Louise-Amélie Schmitt louise-amelie.schm...@embl.de: Well I'm still missing something... Is there a way to use the conditional tag sets in the tool's xml with it? To suppress the unnecessary options for a given file type? or more than one? It sounds like you want to use the

[galaxy-dev] Filter data and cut column bugs

2011-05-23 Thread Peter Cock
Hi all, I filled the following bugs 2 weeks ago, with patches: https://bitbucket.org/galaxy/galaxy-central/issue/537/ Filter data on any column tool casts unused columns https://bitbucket.org/galaxy/galaxy-central/issue/536/ Filter data on any column tools shows nonsense % vs total on stdout

Re: [galaxy-dev] egg install failure: docutils, GeneTrack

2011-05-23 Thread Peter Cock
On Mon, May 16, 2011 at 8:59 PM, Spunde, Alex aspu...@illumina.com wrote: Same thing: [aspunde@ilmnhw-biolin10 galaxy-dist]$ python ./scripts/fetch_eggs.py Fetched http://eggs.g2.bx.psu.edu/Babel/Babel-0.9.4-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/docutils/docutils-0.7-py2.6.egg Fetched

Re: [galaxy-dev] Filter data and cut column bugs

2011-05-23 Thread Peter Cock
On Mon, May 23, 2011 at 3:09 PM, Anton Nekrutenko an...@bx.psu.edu wrote: Dear Peter: Yes, that would help. One possibility would be to have all new bugs CC'd to the dev mailing list? Not sure if everyone here would like that or not... But, you patches are definitely not unnoticed. We'll

Re: [galaxy-dev] Display column headers in data_column parameter

2011-05-24 Thread Peter Cock
On Tue, May 24, 2011 at 3:12 PM, Johannes Eichner johannes.eich...@uni-tuebingen.de wrote: Dear Galaxy-Dev Team, is it possible to display the headers of the columns which can be selected in a data_column parameter? Currently, only the column index (e.g., c1, c2, etc.) is displayed in Galaxy.

  1   2   3   4   5   6   7   8   9   10   >