Tim Reddy Tim [Mon, 24 Nov 2008 18:52:30 +0000 (18:52 +0000)]
Changes the install line to be a copy instead of a move
Rami Rauch [Wed, 19 Nov 2008 19:01:53 +0000 (19:01 +0000)]
converts the HTSW align format (derived from Eland format) into ENCODE 'TagAlign' format
Rami Rauch [Wed, 19 Nov 2008 18:45:58 +0000 (18:45 +0000)]
added: if peak score < zero put zero
Rami Rauch [Fri, 7 Nov 2008 00:44:40 +0000 (00:44 +0000)]
Progress Reports Generator
Rami Rauch [Fri, 7 Nov 2008 00:43:20 +0000 (00:43 +0000)]
Rami Rauch [Wed, 8 Oct 2008 19:44:20 +0000 (19:44 +0000)]
Added a LibInfo folder
Rami Rauch [Wed, 8 Oct 2008 19:43:55 +0000 (19:43 +0000)]
Rami Rauch [Wed, 8 Oct 2008 19:37:58 +0000 (19:37 +0000)]
added updLibInfo function
Rami Rauch [Wed, 8 Oct 2008 19:37:39 +0000 (19:37 +0000)]
added case for calling updLibInfo
Diane Trout [Tue, 7 Oct 2008 22:47:01 +0000 (22:47 +0000)]
update imports for runfolder and eland_makebed for location in htswdataprod.
Rami Rauch [Tue, 7 Oct 2008 21:56:06 +0000 (21:56 +0000)]
Added a display column (not DB) to show the total count of alligned reads for each library record
Diane Trout [Tue, 7 Oct 2008 21:15:42 +0000 (21:15 +0000)]
I moved more of options in settings.py to the .htsworkflow.ini
In this case, the list of admin users were moved to a [admins]
section in the ini file as well as the allowed_ips to [allowed_hosts]
and allowed_analys_ips to [allowed_analysis_hosts].
Currently localhost is always allowed.
Diane Trout [Tue, 7 Oct 2008 21:15:41 +0000 (21:15 +0000)]
I modified the admin base site login page slightly to be less
stanford specific. It would be nice if there was someway of
passing variables to the admin site templates so we could
provide per site branding without having to commit the site
customization to the repository
Diane Trout [Tue, 30 Sep 2008 23:43:26 +0000 (23:43 +0000)]
update imports in srf for htsw directory structure
Diane Trout [Tue, 30 Sep 2008 23:43:25 +0000 (23:43 +0000)]
Pull tool to make srf files from trunk (depends on
util/queuecommands.py)
Diane Trout [Tue, 30 Sep 2008 23:43:23 +0000 (23:43 +0000)]
solexa2srf likes to produce output, so my trick of watching the
sockets to block until when the process ends didn't work.
This patch inserts a simple sleep(1) (second) into the code that
waits for the jobs to finish to prevent the queue manager from rapidly
spinning.
It should probably be fixed with a better way of monitoring for when
a process finishes
MERGED from trunk (the hard way)
Diane Trout [Tue, 30 Sep 2008 22:49:47 +0000 (22:49 +0000)]
add setuptools setup.py scripts for the modules I need to be able to use
Rami Rauch [Mon, 22 Sep 2008 22:33:19 +0000 (22:33 +0000)]
converts QuEST peakcalls output file into narrowPeak ENCODE format
Rami Rauch [Mon, 8 Sep 2008 21:12:49 +0000 (21:12 +0000)]
Removed all Antibody related fields from the Library search_fields list. The Library search for some reason fails to retrieve these records that have NULL in Antibody FK value.
Rami Rauch [Thu, 4 Sep 2008 20:02:39 +0000 (20:02 +0000)]
removed affiliation field from the search_fields option
Rami Rauch [Thu, 4 Sep 2008 20:01:59 +0000 (20:01 +0000)]
Rami Rauch [Thu, 4 Sep 2008 19:18:10 +0000 (19:18 +0000)]
Tim Reddy Tim [Wed, 3 Sep 2008 14:32:09 +0000 (14:32 +0000)]
Updates to profile reads to be more general in how chromosomes are handled
Tim Reddy Tim [Sat, 30 Aug 2008 00:02:32 +0000 (00:02 +0000)]
Added installation notes
Tim Reddy Tim [Fri, 29 Aug 2008 21:44:58 +0000 (21:44 +0000)]
Added MACS source
Diane Trout [Fri, 29 Aug 2008 19:57:49 +0000 (19:57 +0000)]
Change the django settings.py file to get configuration settings from
an ini-like file. Currently it searches, ~/.htsworkflow and
/etc/htsworkflow.ini.
Currently I only implemented the most basic settings overrides needed to
run a django server in development mode.
Tim Reddy Tim [Fri, 29 Aug 2008 18:27:42 +0000 (18:27 +0000)]
Minor typos fixes
Diane Trout [Fri, 29 Aug 2008 17:40:14 +0000 (17:40 +0000)]
Merge in all of my testing code from trunk.
Added a master runtest.sh script that deals with the annoying problem
caused by nesting each package in its own source tree.
I moved in my eland to bed file code (which might still need to be
renamed).
I resolved all the import errors in my illumina specific parsing
code (thanks to the test code)
Diane Trout [Fri, 29 Aug 2008 17:19:52 +0000 (17:19 +0000)]
merge in my changes from trunk
Brandon King [Fri, 29 Aug 2008 17:07:15 +0000 (17:07 +0000)]
Template loading fix.
* Relative path was slightly off.
Diane Trout [Fri, 29 Aug 2008 04:04:17 +0000 (04:04 +0000)]
Ignore *.py[co~] files
Diane Trout [Fri, 29 Aug 2008 00:27:04 +0000 (00:27 +0000)]
return the project xml config file as text/plain so you can read it in
your browser.
Diane Trout [Fri, 29 Aug 2008 00:20:47 +0000 (00:20 +0000)]
update the url matching to provide proper access to the
analys_track/getProject url
Tim Reddy Tim [Thu, 28 Aug 2008 23:39:33 +0000 (23:39 +0000)]
First complete Projects/Tasks build.
Diane Trout [Thu, 28 Aug 2008 22:54:59 +0000 (22:54 +0000)]
Actually the an_urls.py was importing the views, if we remove that
we can remove the views file
Diane Trout [Thu, 28 Aug 2008 22:17:56 +0000 (22:17 +0000)]
Add queuecommand to htswcommon,
add tests for ethelp and queuecommand, though nose will only work
if run from within the htswcommon directory
Rami Rauch [Thu, 28 Aug 2008 21:22:02 +0000 (21:22 +0000)]
cleaned the code a bit: put the method in utils.py
Rami Rauch [Thu, 28 Aug 2008 21:19:35 +0000 (21:19 +0000)]
removed views url
Rami Rauch [Thu, 28 Aug 2008 21:19:03 +0000 (21:19 +0000)]
Diane Trout [Thu, 28 Aug 2008 16:51:44 +0000 (16:51 +0000)]
Django really wanted a view in analys_track, it was periodically
tossing an import error.
I inserted a fairly basic views.py, which seemed to make things better.
Tim Reddy Tim [Thu, 28 Aug 2008 16:46:59 +0000 (16:46 +0000)]
Added a program to help compare libraries
Rami Rauch [Thu, 28 Aug 2008 16:41:01 +0000 (16:41 +0000)]
added Affiliation FK to Libarary + Affiliation table to associate each library record to a project/lab/contact etc..
Brandon King [Thu, 28 Aug 2008 05:21:05 +0000 (05:21 +0000)]
I think this was missing... manage.py is fairly useful. =o)
Rami Rauch [Mon, 25 Aug 2008 22:13:01 +0000 (22:13 +0000)]
added Affiliation table and linked to Library in a ManyToMany relathionship
Rami Rauch [Thu, 21 Aug 2008 22:01:48 +0000 (22:01 +0000)]
small GUI change
Tim Reddy Tim [Thu, 21 Aug 2008 00:47:41 +0000 (00:47 +0000)]
Tasks functionality added. Lots of cleanup to do, but a good start. It remains to test and set up the Projects aspect of the code, which includes reporting html pages on a webserver somewhere.
Tim Reddy Tim [Wed, 20 Aug 2008 21:22:26 +0000 (21:22 +0000)]
Added align_to_bed script. Used to turn MACS output into a bed file
Rami Rauch [Wed, 20 Aug 2008 20:53:07 +0000 (20:53 +0000)]
Rami Rauch [Wed, 20 Aug 2008 20:52:07 +0000 (20:52 +0000)]
Tim Reddy Tim [Wed, 20 Aug 2008 20:39:21 +0000 (20:39 +0000)]
Added wiggle fiole generation
Rami Rauch [Wed, 20 Aug 2008 19:43:29 +0000 (19:43 +0000)]
minor updates
Rami Rauch [Wed, 20 Aug 2008 19:41:54 +0000 (19:41 +0000)]
minor url updates
Rami Rauch [Wed, 20 Aug 2008 19:41:22 +0000 (19:41 +0000)]
the only used function here is makeFCSheet. the other are used for testings.
Rami Rauch [Wed, 20 Aug 2008 19:39:37 +0000 (19:39 +0000)]
minor adjastments
Rami Rauch [Wed, 20 Aug 2008 19:34:09 +0000 (19:34 +0000)]
added Replicate filed in Library table. added as well a 'Short Name' field in Antibody table, to store antigene 'nickname'
Tim Reddy Tim [Wed, 20 Aug 2008 00:47:27 +0000 (00:47 +0000)]
Quest_2_bed conversaion added.
Tim Reddy Tim [Tue, 19 Aug 2008 19:13:20 +0000 (19:13 +0000)]
Added auxillliary programs needed to run projects
Tim Reddy Tim [Tue, 19 Aug 2008 19:09:44 +0000 (19:09 +0000)]
Smalle bug fix
Tim Reddy Tim [Tue, 19 Aug 2008 18:01:43 +0000 (18:01 +0000)]
added comm module of communication.
Tim Reddy Tim [Tue, 19 Aug 2008 18:00:36 +0000 (18:00 +0000)]
Added communitaion between projects and lims
Tim Reddy Tim [Tue, 19 Aug 2008 17:48:28 +0000 (17:48 +0000)]
Initial attempt to get Projects and Tasks framework brought into repository. Lots of work needs to be done gettign directories hooked up and general. Might make sense to start a config files somewhere.
Rami Rauch [Tue, 19 Aug 2008 00:01:01 +0000 (00:01 +0000)]
added search interface to the Task and Project entities. Now, for example, you can search all Projects by LibraryId
Tim Reddy Tim [Mon, 18 Aug 2008 20:12:41 +0000 (20:12 +0000)]
Major bug-fix where some probes in the in-silico qPCR were not working.
Tim Reddy Tim [Mon, 18 Aug 2008 20:12:04 +0000 (20:12 +0000)]
Small change to fix directory structure problem
Rami Rauch [Fri, 15 Aug 2008 22:56:06 +0000 (22:56 +0000)]
These are the template directories and files.
Rami Rauch [Fri, 15 Aug 2008 22:50:00 +0000 (22:50 +0000)]
Replaced 'gaworflow' with 'htsworkflow'; updated settings.py, urls.py etc... Tested: site load sucessfully from /htsworkflow
Brandon King [Fri, 15 Aug 2008 21:43:43 +0000 (21:43 +0000)]
Migrating Rami's frontend changes from stanford branch to htsworkflow branch.
Rami Rauch [Thu, 14 Aug 2008 20:19:34 +0000 (20:19 +0000)]
This text file includes step by step SQL commands to convert your DB into our schema. If used the new htsw_frontend models.py your web site should be able to load your data on the new model.
Tim Reddy Tim [Thu, 14 Aug 2008 19:03:26 +0000 (19:03 +0000)]
Fixed another directory problem: the libraries repo had an assumed location relative to the cwd that is not necessarily true.
Tim Reddy Tim [Thu, 14 Aug 2008 18:59:40 +0000 (18:59 +0000)]
Fixed directories to be more general and easy to set via the environment variable:
HTSW_ANALYSIS_DIR
Tim Reddy Tim [Thu, 14 Aug 2008 18:29:52 +0000 (18:29 +0000)]
Fixed bug that bailed on empty alignment files. (weird exception case)
Tim Reddy Tim [Thu, 14 Aug 2008 18:10:34 +0000 (18:10 +0000)]
Took our some old targets from the Makefile that are going unused.
Tim Reddy Tim [Thu, 14 Aug 2008 17:56:50 +0000 (17:56 +0000)]
Made changes to add quarterly information to the sequencign summary.
Rami Rauch [Wed, 13 Aug 2008 23:54:22 +0000 (23:54 +0000)]
Rami Rauch [Wed, 13 Aug 2008 23:53:53 +0000 (23:53 +0000)]
Rami Rauch [Wed, 13 Aug 2008 23:48:04 +0000 (23:48 +0000)]
Tim Reddy Tim [Wed, 13 Aug 2008 23:45:14 +0000 (23:45 +0000)]
Big steps on getting the library automation going. Small code changes in the qPCR progrm to make output nicer. Then, added a "Makefile" for reference data to get the GenericBackground file used by the qPCR. Lastly, made various changes to correct incorrect paths in the LibrariesMakefile. Stll under testing, but the library system here is becoming funcitonal in the new framework.
Rami Rauch [Wed, 13 Aug 2008 23:20:54 +0000 (23:20 +0000)]
rendered compatible with the updated MPListener
Rami Rauch [Wed, 13 Aug 2008 23:20:16 +0000 (23:20 +0000)]
Rami Rauch [Wed, 13 Aug 2008 23:19:38 +0000 (23:19 +0000)]
rendered compatible with the new MainPipelineScript, which is now ran from runner bot
Rami Rauch [Wed, 13 Aug 2008 23:19:25 +0000 (23:19 +0000)]
rendered compatible with the new MainPipelineScript, which is now ran from runner bot
Rami Rauch [Wed, 13 Aug 2008 23:18:36 +0000 (23:18 +0000)]
rendered completely runnable from runner bot
Unknown Author [Tue, 12 Aug 2008 23:20:17 +0000 (23:20 +0000)]
Unknown Author [Tue, 12 Aug 2008 23:19:38 +0000 (23:19 +0000)]
Unknown Author [Sat, 9 Aug 2008 00:04:26 +0000 (00:04 +0000)]
Finished adding LibraryMakefile related code. Nothing tested yet, but all the necessary source, scripts, and reference data is there. Some parts of LibraryMakefile are commented out until I decide whether to keep them or remove them.
Unknown Author [Fri, 8 Aug 2008 23:44:50 +0000 (23:44 +0000)]
Initial Checkin. Not complete package yet, but a starting point. Bringing in lots of code from various places and making them all talk to each other under a revised directory structure.
Unknown Author [Fri, 8 Aug 2008 23:43:42 +0000 (23:43 +0000)]
Initial Checkin
Unknown Author [Fri, 8 Aug 2008 00:32:48 +0000 (00:32 +0000)]
more dev
Brandon King [Thu, 7 Aug 2008 23:17:51 +0000 (23:17 +0000)]
Need the os module.
Brandon King [Thu, 7 Aug 2008 22:41:24 +0000 (22:41 +0000)]
Update from gaworkflow package to htswdataprod and htswcommon packages.
Brandon King [Thu, 7 Aug 2008 22:40:26 +0000 (22:40 +0000)]
Importing Diane's opener.py from trunk.
Brandon King [Thu, 7 Aug 2008 22:37:57 +0000 (22:37 +0000)]
gaworkflow to htswdataprod package fix.
Brandon King [Thu, 7 Aug 2008 22:36:45 +0000 (22:36 +0000)]
Pulling in Diane's gerald, bustard, and firecrest modules from trunk.
Brandon King [Thu, 7 Aug 2008 21:19:19 +0000 (21:19 +0000)]
Added a Stanford CollectReads compatibility mode.
* Use --compat_mode with --extract-results to trigger this new mdoe.
Brandon King [Thu, 7 Aug 2008 20:24:28 +0000 (20:24 +0000)]
Importing the rest of the code needed for Diane's runfolder.
Brandon King [Thu, 7 Aug 2008 19:55:53 +0000 (19:55 +0000)]
Pulling in Diane's runfolder script from trunk.
Unknown Author [Thu, 7 Aug 2008 00:16:19 +0000 (00:16 +0000)]
continuing the try to make the MainPScript run sucessfully from the bot
Brandon King [Wed, 6 Aug 2008 22:05:44 +0000 (22:05 +0000)]
Progress towards a Stanford runner bot.
Brandon King [Wed, 6 Aug 2008 21:33:30 +0000 (21:33 +0000)]
Migrated exp_track_comm into htswdataprod.exp_track_comm python module.
Brandon King [Wed, 6 Aug 2008 18:19:06 +0000 (18:19 +0000)]
Might actually need the runner_s implementation!