Re: [galaxy-dev] Setting the output label based on input parameters?

2011-08-29 Thread Nikhil Joshi
It looks like the Cheetah syntax only is parsed within the command tags so I figured out a way to do it... but it seems hackish. I basically changed the string values of truevalue and falsevalue within the parameter to be an English sentence that would become the label for the output. I.e.,

[galaxy-dev] API keys and id encryption (silly questions)

2011-08-29 Thread Louise-Amélie Schmitt
Hello everyone, These questions are a bit silly but I'm really ignorant when it comes to security. Sorry about that. Why use API keys instead of user names? Is it to to prevent anyone from figuring out who is behind an URL? Or did I miss the point? Also, why encrypt the

Re: [galaxy-dev] Setting the output label based on input parameters?

2011-08-29 Thread Ross
On Thu, Aug 25, 2011 at 6:34 AM, SHAUN WEBB swe...@staffmail.ed.ac.uk wrote: I meant to say label=${input} or label=${input.value}. Nikhil, did you try as Shaun and others have suggested? Any available string parameter can be used in a label as far as I can tell. This is a common idiom -

Re: [galaxy-dev] next galaxy-dist update

2011-08-29 Thread Glen Beane
Bump! We want to upgrade to get some of the newer features (since we skipped the last dist update), but we don't want to upgrade now and then have a new dist release in a few days. Can any developer comment on the timeline for the next Galaxy dist release? On Aug 23, 2011, at 8:32 AM, Glen

Re: [galaxy-dev] migrate the database schema from 80 to 81

2011-08-29 Thread Nate Coraor
Jack Zhu wrote: Hi all, I have problems with updating my local instance of Galaxy. Specifically I can not migrate the database schema from 80 to 81: Hi Jack, Thanks for reporting this issue. It has been fixed in changeset 5951:62d51750d7df. --nate -- $$ sh manage_db.sh

[galaxy-dev] contribute tools to galaxy?

2011-08-29 Thread Dongjun Chung
Hi All, I'm a newbie to galaxy and enjoying it a lot these days. Thanks for the great work. I have a question regarding contribution of software to galaxy. We developed a ChIP-seq peak calling algorithm and software (R package) and hope to contribute it to galaxy. I have read the wiki and prior

[galaxy-dev] contribute tools to galaxy?

2011-08-29 Thread Dongjun Chung
Hi All, I'm a newbie to galaxy and enjoying it a lot these days. Thanks for the great work. I have a question regarding contribution of software to galaxy. We developed a ChIP-seq peak calling algorithm and software (R package) and hope to contribute it to galaxy. I have read the wiki and prior

Re: [galaxy-dev] API keys and id encryption (silly questions)

2011-08-29 Thread Nate Coraor
Louise-Amélie Schmitt wrote: Hello everyone, These questions are a bit silly but I'm really ignorant when it comes to security. Sorry about that. Why use API keys instead of user names? Is it to to prevent anyone from figuring out who is behind an URL? Or did I miss the point? Hi L-A,

Re: [galaxy-dev] next galaxy-dist update

2011-08-29 Thread Nate Coraor
It's looking like tomorrow or Wednesday at this point. We're working on the new feature documentation and news brief right now. --nate Glen Beane wrote: Bump! We want to upgrade to get some of the newer features (since we skipped the last dist update), but we don't want to upgrade now and

Re: [galaxy-dev] install with EPD python?

2011-08-29 Thread Nate Coraor
Paul Tanger wrote: Yes it works with the default python install. Any way I can get it working with EPD python? I've never worked with EPD and since it's not free it's unlikely we can do much debugging on it here. It would appear that they bundle a version of pkg_resources which changes the

Re: [galaxy-dev] Galaxy Test disk quota

2011-08-29 Thread Nate Coraor
Crystal Goh wrote: Dear Nate, Thanks. I used multiple account as I have several csfasta and qual files and each file is large in size. My account is gohweip...@hotmail.com. Can I get increement for disk quota for this account so that I can used only 1 account that can proceess

Re: [galaxy-dev] install with EPD python?

2011-08-29 Thread Paul Tanger
It is free for academic use. I'll try what you suggested below - thanks! On Mon, Aug 29, 2011 at 7:59 AM, Nate Coraor n...@bx.psu.edu wrote: Paul Tanger wrote: Yes it works with the default python install. Any way I can get it working with EPD python? I've never worked with EPD and

Re: [galaxy-dev] install with EPD python?

2011-08-29 Thread Paul Tanger
sys path is: ['/Users/paultanger/galaxy-dist/scripts', '/Users/paultanger/python/scripts', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python26.zip', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6',

Re: [galaxy-dev] [API] Error message forwarding

2011-08-29 Thread Nate Coraor
Louise-Amélie Schmitt wrote: Hi, I ran into a little something that is a bit annoying for debug when trying to upload files through the API with library_upload_from_import_dir.py. When the specified folder is wrong, python tries to process the error tuple like a dict, so the original error

Re: [galaxy-dev] API keys and id encryption (silly questions)

2011-08-29 Thread Louise-Amélie Schmitt
Le 29/08/2011 15:52, Nate Coraor a écrit : Louise-Amélie Schmitt wrote: Hello everyone, These questions are a bit silly but I'm really ignorant when it comes to security. Sorry about that. Why use API keys instead of user names? Is it to to prevent anyone from figuring out who is behind an

[galaxy-dev] mycoplasma genomes - suggestion

2011-08-29 Thread Lukasz Kielpinski
Hello everybody, I would like to suggest including mycoplasma genomes (preferably all genomes in one file) as reference genomes. It would enable fast checking if cells used for deep-seq experiments were not contaminated. Best, Lukasz ___

Re: [galaxy-dev] install with EPD python?

2011-08-29 Thread Nate Coraor
Paul Tanger wrote: sys path is: ['/Users/paultanger/galaxy-dist/scripts', '/Users/paultanger/python/scripts', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python26.zip', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6',

Re: [galaxy-dev] install with EPD python?

2011-08-29 Thread Paul Tanger
Getting somewhere, but it looks like it can't find numpy 1.6? error returned is: pkg_resources is: module 'pkg_resources' from '/Users/paultanger/galaxy-dist/lib/pkg_resources.py' Some eggs are out of date, attempting to fetch... pkg_resources is: module 'pkg_resources' from

Re: [galaxy-dev] install with EPD python?

2011-08-29 Thread Nate Coraor
Paul Tanger wrote: Getting somewhere, but it looks like it can't find numpy 1.6? error returned is: pkg_resources is: module 'pkg_resources' from '/Users/paultanger/galaxy-dist/lib/pkg_resources.py' Some eggs are out of date, attempting to fetch... pkg_resources is: module

Re: [galaxy-dev] API keys and id encryption (silly questions)

2011-08-29 Thread Nate Coraor
Louise-Amélie Schmitt wrote: Le 29/08/2011 15:52, Nate Coraor a écrit : Louise-Amélie Schmitt wrote: Hello everyone, These questions are a bit silly but I'm really ignorant when it comes to security. Sorry about that. Why use API keys instead of user names? Is it to to prevent anyone

Re: [galaxy-dev] install with EPD python?

2011-08-29 Thread Paul Tanger
That worked, for everything but pysam. I also tried to install it directly: pysam 0.4.2 couldn't be downloaded automatically. You can try building it by hand with: python scripts/scramble.py -e pysam Some eggs are out of date, attempting to fetch... pkg_resources is: module 'pkg_resources'

Re: [galaxy-dev] Galaxy Test disk quota

2011-08-29 Thread Crystal Goh
Dear Nate, Thank you very much. Best regards, Crystal Date: Mon, 29 Aug 2011 10:04:21 -0400 From: n...@bx.psu.edu To: crysta...@live.com.my CC: galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Galaxy Test disk quota Crystal Goh wrote: Dear Nate, Thanks. I used

Re: [galaxy-dev] install with EPD python?

2011-08-29 Thread Nate Coraor
Paul Tanger wrote: That worked, for everything but pysam. I also tried to install it directly: pysam 0.4.2 couldn't be downloaded automatically. You can try building it by hand with: python scripts/scramble.py -e pysam Some eggs are out of date, attempting to fetch...

Re: [galaxy-dev] install with EPD python?

2011-08-29 Thread Paul Tanger
I don't know if I did this correctly, but the output from python get_platforms.py is: macosx-10.5-i386-ucs2 On Mon, Aug 29, 2011 at 12:13 PM, Nate Coraor n...@bx.psu.edu wrote: Paul Tanger wrote: That worked, for everything but pysam. I also tried to install it directly: pysam 0.4.2

Re: [galaxy-dev] install with EPD python?

2011-08-29 Thread Nate Coraor
Paul Tanger wrote: I don't know if I did this correctly, but the output from python get_platforms.py is: macosx-10.5-i386-ucs2 Okay, it looks like EPD python is only compiled for one platform. To use this, you'll need to scramble your own versions of the eggs which use C code. Could you try

Re: [galaxy-dev] Display BAM with IGV

2011-08-29 Thread Nate Coraor
Iry Witham wrote: Hi Nate, I have been able to get this to work on a Mac and Windows XP within limited guide lines. The following are what I had to do to make it work: My Mac is now running Java 1.6.0_26, Firefox 3.6.20, Google Crome ver.13.0.782.215 and Safari 5.1 (6534.50). In

[galaxy-dev] Galaxy is Hiring

2011-08-29 Thread Dave Clements
Hello all The Galaxy Project is growing and has open positions in both the Penn State and Emory groups (http://wiki.g2.bx.psu.edu/News/Galaxy%20is%20Hiring). *Penn State: System administrators/analysts* The Nekrutenko Lab http://www.bx.psu.edu/%7Eanton/ at the Huck Institutes of Life Sciences

Re: [galaxy-dev] Setting the output label based on input parameters?

2011-08-29 Thread Nikhil Joshi
Hi Ross, Yes, I did try that... but what I want is string parameter that changes based on whether or not you've checked a checkbox (or a way to change the label of the output based on whether or not the checkbox was checked). So my idea below did work, but it seems like a hack. Which is why I

Re: [galaxy-dev] Setting the output label based on input parameters?

2011-08-29 Thread Ross
Most times I need a user supplied label substring. I'm not sure how else to conditionally set a string to a predetermined value other than with boolean true/false strings or select parameter values. One even more ugly option is to use a (strictly speaking now deprecated) post job exec hook to

Re: [galaxy-dev] migrate the database schema from 80 to 81

2011-08-29 Thread Jack Zhu
Hi Nate, Thanks for the fix. Everything is working great now. Jack On 29 August 2011 09:33, Nate Coraor n...@bx.psu.edu wrote: Jack Zhu wrote: Hi all, I have problems with updating my local instance of Galaxy. Specifically I can not migrate the database schema from 80 to 81: Hi Jack,