[galaxy-dev] pass more information on a dataset merge

2012-10-01 Thread Jorrit Boekel
Dear list, I thought I was working with fairly large datasets, but they have recently started to include ~2Gb files in sets of >50. I have ran these sort of things before as merged data by using tar to roll them up in one set, but when dealing with >100Gb tarfiles, Galaxy on EC2 seems to get

[galaxy-dev] Coupling the output of two tools

2012-10-01 Thread Robert Chase
Hello, We added batch gfPcr as a tool in galaxy by writing a wrapper. We wrote another tool in python to modify the output of this tool (we increment the starts of the intervals by 1 to make the starting intervals 1 based) and wrote a wrapper for this other tool. Is is possible to couple these too

Re: [galaxy-dev] Coupling the output of two tools

2012-10-01 Thread Peter Cock
On Fri, Sep 28, 2012 at 11:28 PM, Robert Chase wrote: > Hello, > > We added batch gfPcr as a tool in galaxy by writing a wrapper. We wrote > another tool in python to modify the output of this tool (we increment the > starts of the intervals by 1 to make the starting intervals 1 based) and > wrote

Re: [galaxy-dev] HYPHY tools

2012-10-01 Thread Nate Coraor
On Sep 10, 2012, at 6:29 PM, Julian Pradinuk wrote: > Hi all, > > Could someone please point me to helpful ressources for installing HYPHY in > Galaxy? > > • I've downloaded, compiled and installed HyPhy > • I've copied the contents of the installation folder to > .../galaxy-dist/t

Re: [galaxy-dev] LDAP integration and migration of users

2012-10-01 Thread Nate Coraor
On Sep 11, 2012, at 5:01 AM, Joachim Jacob wrote: > Hi all, > > I wonder if somebody with experience could enlighten me on these issues > regarding authentication of users. > > - is it possible to have LDAP integration simultaneously with local Galaxy > users. What I want to reach is when LDAP

Re: [galaxy-dev] markupsafe module conflicts

2012-10-01 Thread Nate Coraor
On Sep 11, 2012, at 12:09 PM, Fenglou Mao wrote: > Galaxy imported a library which already existed in the python system folder. > See the error message below. > > /home/x/work/galaxy-dist/lib/galaxy/__init__.py:79: UserWarning: Module > markupsafe was already imported from > /usr/lib64/pyt

Re: [galaxy-dev] Size of the genome indexes repos in Galaxy Main

2012-10-01 Thread Nate Coraor
On Sep 20, 2012, at 7:55 AM, Derrick Lin wrote: > Hi Nate, > > We downloaded the entire indexes repos and our guys are planning to write a > script to generate loc files based on the given path to the repos. > > We are wondering if the galaxy team will release the loc files that are being > us

Re: [galaxy-dev] Orphan dataset created by history Export to File (possibly a bug?)

2012-10-01 Thread Nate Coraor
Hi Derrick, If you're using Postgres, it's now possible to clean these up using galaxy-dist/scripts/cleanup_datasets/pgcleanup.py --nate On Sep 13, 2012, at 11:55 PM, Derrick Lin wrote: > Thanks Jeremy, > > I am sure it's trivial for us to do a manual clean up > > Cheers, > D > > On Fri, Se

Re: [galaxy-dev] Issues up/downloading datasets after file_path change

2012-10-01 Thread Nate Coraor
Hi Josh, Are you using XSendFile or X-Accel-Redirect, by any chance? --nate On Sep 17, 2012, at 5:18 PM, Josh Nielsen wrote: > Okay, I solved half of the problem. The upload job was consistently being > submitted to the one compute node in our cluster that I forgot to create the > symlink on

Re: [galaxy-dev] speed and large file question (after tying galaxy to Pittsburgh)

2012-10-01 Thread Nate Coraor
On Sep 18, 2012, at 11:56 AM, Joseph Hargitai wrote: > Hi, > > General: > Is there a quantifiable difference in data uploads, speed of processing, > general availability after the connection was/is established to Pittsburgh? Hi Joe, I haven't tested it within the front end of Galaxy to see whe

Re: [galaxy-dev] Orphan dataset created by history Export to File (possibly a bug?)

2012-10-01 Thread Langhorst, Brad
On Oct 1, 2012, at 12:16 PM, Nate Coraor wrote: > Hi Derrick, > > If you're using Postgres, it's now possible to clean these up using > galaxy-dist/scripts/cleanup_datasets/pgcleanup.py > I hope this is not considered hijacking… I just tried to run the pgcleanup.py script and got this erro

[galaxy-dev] October 2012 Galaxy Update

2012-10-01 Thread Dave Clements
Hello all, The October 2012 Galaxy Update is now available :** - Upcoming Events and Deadlines - 35 new papers

Re: [galaxy-dev] Error when running cleanup_datasets.py

2012-10-01 Thread Nate Coraor
On Sep 24, 2012, at 10:41 AM, Liisa Koski wrote: > Hello, > I am trying to run the cleanup scripts on my local installation but get stuck > when trying to run the following: > > ./scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -d 10 -5 -r > > Deleting library dataset id 7225

Re: [galaxy-dev] Orphan dataset created by history Export to File (possibly a bug?)

2012-10-01 Thread Nate Coraor
On Oct 1, 2012, at 12:50 PM, Langhorst, Brad wrote: > > On Oct 1, 2012, at 12:16 PM, Nate Coraor > wrote: > >> Hi Derrick, >> >> If you're using Postgres, it's now possible to clean these up using >> galaxy-dist/scripts/cleanup_datasets/pgcleanup.py >> > > I hope this is not considered hija

[galaxy-dev] Jeremy's DataProvider changes

2012-10-01 Thread Ted Goldstein
I just saw the new Data Provider changes. Is still looks very focused on genomic data needed by Trackster.I would like to have a general mechanism for generating heatmaps for systems biology. We need similar separation of data and presentation. Should we consider the new API? Thanks Ted

Re: [galaxy-dev] Jeremy's DataProvider changes

2012-10-01 Thread James Taylor
It is definitely intended to be general (I believe there is a column data provider intended for scatterplot visualizations that should land soon). We definitely want this to be general enough to use for any visualization, so please consider this API and help us to make it as general as appropriate.

Re: [galaxy-dev] How to rotate Galaxy log file

2012-10-01 Thread Lance Parsons
I also use a logrotate script: '/etc/logrotate.d/galaxy' /path/to/galaxy/install/*.log { weekly rotate 52 copytruncate } The 'compress' options seems like it might be nice, and I'm not sure of the effect of size 1. I don't think the 'create 640 galaxy-user galaxy-group' has an

Re: [galaxy-dev] How to rotate Galaxy log file

2012-10-01 Thread Shantanu Pavgi
On Oct 1, 2012, at 2:57 PM, Lance Parsons wrote: > I also use a logrotate script: '/etc/logrotate.d/galaxy' > > /path/to/galaxy/install/*.log { > weekly > rotate 52 > copytruncate > } > > > The 'compress' options seems like it might be nice, and I'm not sure of the > effect of siz

Re: [galaxy-dev] Orphan dataset created by history Export to File (possibly a bug?)

2012-10-01 Thread Derrick Lin
Sorry Nate, We are using MySQL so cannot verify this. We are happy to try once the MySQL alternative's released. Regards, Derrick On Tue, Oct 2, 2012 at 2:16 AM, Nate Coraor wrote: > Hi Derrick, > > If you're using Postgres, it's now possible to clean these up using > galaxy-dist/scripts/clean

[galaxy-dev] Galaxy workflow editor cannot be loaded due to some JS files received 404 not found

2012-10-01 Thread Derrick Lin
Hi guys, We just discovered this issue on our new production galaxy. When trying to open the workflow editor, the page just stuck in the loading bar. I opened the JavaScript debug console of the web browser, I found; GET http://pwbcglxprod:8081/galaxy/static/scripts/jquery.js?v=1348871183404 (Not