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NGS peak calling: MACS
by Claudia Cattoglio 22 Apr '10

22 Apr '10

Hi, I am trying to use MACS among your NGS peak-calling tools, but I can't work it out. I have ELAND files; what should I specify as a file format when uploading them? There is no ELAND format in the 'upload file' window. If I choose BED as a format, after running MACS I get no results (empty) and a Strand Format Error message, although I am sure the strand information in my ELAND file is correct (9th column, F or R). If I choose TABULAR, instead, my files are not even visualized in the MACS dropdown menu. Is this a problem of input file format, as I suspect? Thanks, Claudia Cattoglio, PhD Tjian Lab University of California, Berkeley Department of Molecular & Cell Biology 16 Barker Hall # 3204 Berkeley, CA 94720-3204 phone: (510) 643-3762

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any plans to incorporate GSAssembler into Galaxy?
by Kevin Silverstein 21 Apr '10

21 Apr '10

Hi all, I was wondering if anyone has plans to incorporate GSAssembler for Roche 454 sequence assembly? If no one else is doing this, I will try my hand at it over the next couple months since I need this for my processing pipeline. But, obviously, if this is already in the works and will be done over the next two months horizon, there is no point in my reinventing the wheel. Thanks, Kevin

2 1

Galaxy update problem
by Martin Paradesi 19 Apr '10

19 Apr '10

Hello, We have been running a local mirror of Galaxy on our cluster for few months now. Recently, I went ahead and updated the local repository using "hg pull -u". After attempting to run the latest version, I found out that SGE was updated to 6.2u5 (from 6.2u3). We compiled the DRMAA_python egg for Galaxy, but unfortunately we are unable to access it over the browser. The problem is that ToolRunner controller fails (as shown below) and Galaxy is not served via http. Here's the log: galaxy.jobs INFO 2010-04-09 13:19:28,003 job stopper started galaxy.web.framework.base DEBUG 2010-04-09 13:19:28,056 Enabling 'admin' controller, class: Admin galaxy.web.framework.base DEBUG 2010-04-09 13:19:28,063 Enabling 'async' controller, class: ASync galaxy.web.framework.base DEBUG 2010-04-09 13:19:28,265 Enabling 'cloud' controller, class: CloudController galaxy.web.framework.base DEBUG 2010-04-09 13:19:28,337 Enabling 'dataset' controller, class: DatasetInterface galaxy.web.framework.base DEBUG 2010-04-09 13:19:28,342 Enabling 'error' controller, class: Error galaxy.web.framework.base DEBUG 2010-04-09 13:19:28,354 Enabling 'forms' controller, class: Forms galaxy.web.framework.base DEBUG 2010-04-09 13:19:28,367 Enabling 'history' controller, class: HistoryController galaxy.web.framework.base DEBUG 2010-04-09 13:19:28,371 Enabling 'library' controller, class: Library galaxy.web.framework.base DEBUG 2010-04-09 13:19:28,376 Enabling 'library_admin' controller, class: LibraryAdmin galaxy.web.framework.base DEBUG 2010-04-09 13:19:28,398 Enabling 'library_common' controller, class: LibraryCommon galaxy.web.framework.base DEBUG 2010-04-09 13:19:28,402 Enabling 'mobile' controller, class: Mobile galaxy.web.framework.base DEBUG 2010-04-09 13:19:28,407 Enabling 'page' controller, class: PageController galaxy.web.framework.base DEBUG 2010-04-09 13:19:28,411 Enabling 'requests' controller, class: Requests galaxy.web.framework.base DEBUG 2010-04-09 13:19:28,440 Enabling 'requests_admin' controller, class: RequestsAdmin galaxy.web.framework.base DEBUG 2010-04-09 13:19:28,445 Enabling 'root' controller, class: RootController galaxy.web.framework.base DEBUG 2010-04-09 13:19:28,449 Enabling 'tag' controller, class: TagsController galaxy.web.framework.base DEBUG 2010-04-09 13:19:28,453 Enabling 'tool_runner' controller, class: ToolRunner Traceback (most recent call last): File "./scripts/paster.py", line 34, in <module> command.run() File "/LOCATION/galaxy/eggs/PasteScript-1.7.3-py2.5.egg/paste/script/command.py", line 84, in run invoke(command, command_name, options, args[1:]) File "/LOCATION/galaxy/eggs/PasteScript-1.7.3-py2.5.egg/paste/script/command.py", line 123, in invoke exit_code = runner.run(args) File "/LOCATION/galaxy/eggs/PasteScript-1.7.3-py2.5.egg/paste/script/command.py", line 218, in run result = self.command() File "/LOCATION/galaxy/eggs/PasteScript-1.7.3-py2.5.egg/paste/script/serve.py", line 276, in command relative_to=base, global_conf=vars) File "/LOCATION/galaxy/eggs/PasteScript-1.7.3-py2.5.egg/paste/script/serve.py", line 313, in loadapp **kw) File "/LOCATION/galaxy/eggs/PasteDeploy-1.3.3-py2.5.egg/paste/deploy/loadwsgi.py", line 204, in loadapp return loadobj(APP, uri, name=name, **kw) File "/LOCATION/galaxy/eggs/PasteDeploy-1.3.3-py2.5.egg/paste/deploy/loadwsgi.py", line 225, in loadobj return context.create() File "/LOCATION/galaxy/eggs/PasteDeploy-1.3.3-py2.5.egg/paste/deploy/loadwsgi.py", line 625, in create return self.object_type.invoke(self) File "/LOCATION/galaxy/eggs/PasteDeploy-1.3.3-py2.5.egg/paste/deploy/loadwsgi.py", line 188, in invoke filtered = context.next_context.create() File "/LOCATION/galaxy/eggs/PasteDeploy-1.3.3-py2.5.egg/paste/deploy/loadwsgi.py", line 625, in create return self.object_type.invoke(self) File "/LOCATION/galaxy/eggs/PasteDeploy-1.3.3-py2.5.egg/paste/deploy/loadwsgi.py", line 110, in invoke return fix_call(context.object, context.global_conf, **context.local_conf) File "/LOCATION/galaxy/eggs/PasteDeploy-1.3.3-py2.5.egg/paste/deploy/util/fixtypeerror.py", line 57, in fix_call val = callable(*args, **kw) File "/LOCATION/galaxy/lib/galaxy/web/buildapp.py", line 69, in app_factory add_controllers( webapp, app ) File "/LOCATION/galaxy/lib/galaxy/web/buildapp.py", line 39, in add_controllers module = __import__( module_name ) File "/LOCATION/galaxy/lib/galaxy/web/controllers/tracks.py", line 27, in <module> from galaxy.visualization.tracks.data.bam import BamDataProvider File "/LOCATION/galaxy/lib/galaxy/visualization/tracks/data/bam.py", line 7, in <module> from pysam import csamtools File "/usr/lib/python-2.5.2/lib/python2.5/site-packages/PIL/__init__.py", line 1, in <module> # File "build/bdist.linux-x86_64-ucs2/egg/pysam/csamtools.py", line 7, in <module> File "build/bdist.linux-x86_64-ucs2/egg/pysam/csamtools.py", line 6, in __bootstrap__ ImportError: /HOME_LOCATION/.python-eggs/pysam-0.1.1_kanwei_90e03180969d-py2.5-linux-x86_64-ucs2.egg-tmp/pysam/csamtools.so: undefined symbol: deflateSetHeader Your help will be greatly appreciated. Thanks, Martin

1 0

Problems with lims
by nsfox＠uwaterloo.ca 16 Apr '10

16 Apr '10

Hi, I just updated my galaxy instance and there is a few things that aren't working. 1. Whenever I try to transfer a file from a sequencing request I am getting the error Error.The user1(a)example.org user could not login to Galaxy 2. one of the update emails was "lims: required fields of samples are now enforced by submission" but I still don't seem to have this functionality 3. When importing the form fields from a csv file the fields are not being assigned to the grid level that they are specified for. This was true before I updated the instance. Let me know if you have any ideas for me to fix this issues. Thanks, Natalie

2 2

[hg] galaxy 3662: forgot rgcaco - stretch lines_diff
by Greg Von Kuster 16 Apr '10

16 Apr '10

details: http://www.bx.psu.edu/hg/galaxy/rev/6be8d5818087 changeset: 3662:6be8d5818087 user: fubar: ross Lazarus at gmail period com date: Thu Apr 15 21:41:50 2010 -0400 description: forgot rgcaco - stretch lines_diff diffstat: tools/rgenetics/rgCaCo.xml | 2 +- 1 files changed, 1 insertions(+), 1 deletions(-) diffs (12 lines): diff -r 92ce16e0e37e -r 6be8d5818087 tools/rgenetics/rgCaCo.xml --- a/tools/rgenetics/rgCaCo.xml Thu Apr 15 21:20:04 2010 -0400 +++ b/tools/rgenetics/rgCaCo.xml Thu Apr 15 21:41:50 2010 -0400 @@ -31,7 +31,7 @@ </param> <param name='name' value='rgCaCotest1' /> <output name='out_file1' file='rgCaCotest1_CaCo.xls' ftype='tabular' compare='diff' /> - <output name='logf' file='rgCaCotest1_CaCo_log.txt' ftype='txt' compare='diff' lines_diff='19' /> + <output name='logf' file='rgCaCotest1_CaCo_log.txt' ftype='txt' compare='diff' lines_diff='20' /> <output name='gffout' file='rgCaCotest1_CaCo_topTable.gff' ftype='gff' compare='diff' /> </test> </tests>

1 0

[hg] galaxy 3661: Less blather from rgGRR and new functional tes...
by Greg Von Kuster 16 Apr '10

16 Apr '10

details: http://www.bx.psu.edu/hg/galaxy/rev/92ce16e0e37e changeset: 3661:92ce16e0e37e user: fubar: ross Lazarus at gmail period com date: Thu Apr 15 21:20:04 2010 -0400 description: Less blather from rgGRR and new functional test output files to match Stretch lines_diff even further to accomodate an older version of plink for functional tests diffstat: lib/galaxy/datatypes/genetics.py | 24 +- test-data/rgtestouts/rgGRR/Log_rgGRRtest1.txt | 21 +- test-data/rgtestouts/rgGRR/rgGRRtest1.html | 32 +- test-data/rgtestouts/rgGRR/rgGRRtest1.svg | 517 +------ test-data/rgtestouts/rgGRR/rgGRRtest1_table.xls | 1560 +++++++++++----------- test-data/smallwgaP.xls | 103 + tools/rgenetics/rgGLM.xml | 2 +- tools/rgenetics/rgGRR.py | 8 +- tools/rgenetics/rgGRR.xml | 2 +- tools/rgenetics/rgQC.xml | 2 +- 10 files changed, 967 insertions(+), 1304 deletions(-) diffs (2456 lines): diff -r ed5535c4d48e -r 92ce16e0e37e lib/galaxy/datatypes/genetics.py --- a/lib/galaxy/datatypes/genetics.py Thu Apr 15 15:58:08 2010 -0400 +++ b/lib/galaxy/datatypes/genetics.py Thu Apr 15 21:20:04 2010 -0400 @@ -86,8 +86,6 @@ site_url = site_url.replace('/hgTracks?','/hgGenome?') # for genome graphs internal_url = "%s" % url_for( controller='dataset', dataset_id=dataset.id, action='display_at', filename='ucsc_' + site_name ) - if base_url.startswith( 'https://' ): - base_url = base_url.replace( 'https', 'http', 1 ) display_url = "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" % (base_url, url_for( controller='root' ), dataset.id, type) display_url = urllib.quote_plus( display_url ) # was display_url = urllib.quote_plus( "%s/display_as?id=%i&display_app=%s" % (base_url, dataset.id, type) ) @@ -264,7 +262,7 @@ stored in extra files path """ - MetadataElement( name="base_name", desc="base name for all transformed versions of this genetic dataset", default="rgenetics", + MetadataElement( name="base_name", desc="base name for all transformed versions of this genetic dataset", readonly=True, set_in_upload=True) composite_type = 'auto_primary_file' @@ -290,27 +288,15 @@ """ cannot do this until we are setting metadata """ - guessmt = {'.log':'text/plain','.ped':'text/plain', '.map':'text/plain','.out':'text/plain','.in':'text/plain'} - def fix(oldpath,newbase): - old,e = os.path.splitext(oldpath) - head,rest = os.path.split(old) - newpath = os.path.join(head,newbase) - newpath = '%s%s' % (newpath,e) - if oldpath <> newpath: - shutil.move(oldpath,newpath) - return newpath bn = dataset.metadata.base_name efp = dataset.extra_files_path flist = os.listdir(efp) - proper_base = bn - rval = ['<html><head><title>Files for Composite Dataset %s</title></head><p/>Composite %s contains the following files:<p/><ul>' % (dataset.name,dataset.name)] + rval = ['<html><head><title>Files for Composite Dataset %s</title></head><body><p/>Composite %s contains:<p/><ul>' % (dataset.name,dataset.name)] for i,fname in enumerate(flist): - newpath = fix(os.path.join(efp,fname),proper_base) - sfname = os.path.split(newpath)[-1] + sfname = os.path.split(fname)[-1] f,e = os.path.splitext(fname) - mt = guessmt.get(e,'application/binary') - rval.append( '<li><a href="%s" mimetype="%s">%s</a></li>' % ( sfname, mt, sfname) ) - rval.append( '</ul></html>' ) + rval.append( '<li><a href="%s">%s</a></li>' % ( sfname, sfname) ) + rval.append( '</ul></body></html>' ) f = file(dataset.file_name,'w') f.write("\n".join( rval )) f.write('\n') diff -r ed5535c4d48e -r 92ce16e0e37e test-data/rgtestouts/rgGRR/Log_rgGRRtest1.txt --- a/test-data/rgtestouts/rgGRR/Log_rgGRRtest1.txt Thu Apr 15 15:58:08 2010 -0400 +++ b/test-data/rgtestouts/rgGRR/Log_rgGRRtest1.txt Thu Apr 15 21:20:04 2010 -0400 @@ -1,22 +1,13 @@ -Reading genotypes for 40 subjects and 25 markers -Calculating 780 pairs, updating every 78 pairs... +Reading genotypes for 40 subjects and 5 markers +Calculating 780 pairs... Estimated time is 0.00 to 0.00 seconds ... -0.003503 sec at pair 78 of 780 (10.00%): 556652.337848 marker*pairs/sec -0.005636 sec at pair 156 of 780 (20.00%): 691982.977283 marker*pairs/sec -0.007769 sec at pair 234 of 780 (30.00%): 752982.213220 marker*pairs/sec -0.009869 sec at pair 312 of 780 (40.00%): 790345.731265 marker*pairs/sec -0.011900 sec at pair 390 of 780 (50.00%): 819314.887905 marker*pairs/sec -0.013981 sec at pair 468 of 780 (60.00%): 836843.791886 marker*pairs/sec -0.015971 sec at pair 546 of 780 (70.00%): 854664.262256 marker*pairs/sec -0.017976 sec at pair 624 of 780 (80.00%): 867821.563192 marker*pairs/sec -0.020017 sec at pair 702 of 780 (90.00%): 876748.317016 marker*pairs/sec -T1: 0.00267601013184 T2: 0.0181350708008 T3: 0.000470638275146 TOT: 0.0224170684814 0 pairs with no (or not enough) comparable genotypes (0.0%) +T1: 0.00229454040527 T2: 0.0166795253754 T3: 0.000442743301392 TOT: 0.0201091766357 0 pairs with no (or not enough) comparable genotypes (0.0%) Relstate dupe: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00 -Relstate parentchild: mean(mean)=1.68 sdev(mean)=0.19, mean(sdev)=0.39 sdev(sdev)=0.19 +Relstate parentchild: mean(mean)=1.82 sdev(mean)=0.14, mean(sdev)=0.33 sdev(sdev)=0.22 Relstate sibpairs: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00 Relstate halfsibs: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00 -Relstate parents: mean(mean)=1.46 sdev(mean)=0.25, mean(sdev)=0.55 sdev(sdev)=0.17 -Relstate unrelated: mean(mean)=1.44 sdev(mean)=0.21, mean(sdev)=0.58 sdev(sdev)=0.15 +Relstate parents: mean(mean)=1.62 sdev(mean)=0.21, mean(sdev)=0.53 sdev(sdev)=0.29 +Relstate unrelated: mean(mean)=1.60 sdev(mean)=0.23, mean(sdev)=0.54 sdev(sdev)=0.22 Relstate unknown: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00 780 pairs are available of 780 Outliers: 0 diff -r ed5535c4d48e -r 92ce16e0e37e test-data/rgtestouts/rgGRR/rgGRRtest1.html --- a/test-data/rgtestouts/rgGRR/rgGRRtest1.html Thu Apr 15 15:58:08 2010 -0400 +++ b/test-data/rgtestouts/rgGRR/rgGRRtest1.html Thu Apr 15 21:20:04 2010 -0400 @@ -9,7 +9,7 @@ </head> <body> <div class="document"> -<h4><div>Output from rgGRR.py run at 25/03/2010 21:01:24<br> +<h4><div>Output from rgGRR.py run at 15/04/2010 13:12:45<br> </h4> If you need to rerun this analysis, the command line was <pre>'/opt/galaxy/tools/rgenetics/rgGRR.py' '/opt/galaxy/test-data/tinywga' 'tinywga' '/opt/galaxy/test-data/rgtestouts/rgGRR/rgGRRtest1.html' '/opt/galaxy/test-data/rgtestouts/rgGRR' 'rgGRRtest1' '100' '6'</pre> @@ -18,43 +18,25 @@ <li><a href="rgGRRtest1_table.xls">Mean by SD alleles shared - 780 rows</a></li> <li><a href="rgGRRtest1.html">rgGRRtest1.html</a></li> <li><a href="Log_rgGRRtest1.txt">Log_rgGRRtest1.txt</a></li> -</ol></div><div><h2>Outliers in tab delimited files linked above are also listed below</h2></div><div><hr><h3>Log from this job (also stored in Log_rgGRRtest1.txt)</h3><pre>Reading genotypes for 40 subjects and 25 markers +</ol></div><div><h2>Outliers in tab delimited files linked above are also listed below</h2></div><div><hr><h3>Log from this job (also stored in Log_rgGRRtest1.txt)</h3><pre>Reading genotypes for 40 subjects and 5 markers -Calculating 780 pairs, updating every 78 pairs... +Calculating 780 pairs... Estimated time is 0.00 to 0.00 seconds ... -0.003503 sec at pair 78 of 780 (10.00%): 556652.337848 marker*pairs/sec - -0.005636 sec at pair 156 of 780 (20.00%): 691982.977283 marker*pairs/sec - -0.007769 sec at pair 234 of 780 (30.00%): 752982.213220 marker*pairs/sec - -0.009869 sec at pair 312 of 780 (40.00%): 790345.731265 marker*pairs/sec - -0.011900 sec at pair 390 of 780 (50.00%): 819314.887905 marker*pairs/sec - -0.013981 sec at pair 468 of 780 (60.00%): 836843.791886 marker*pairs/sec - -0.015971 sec at pair 546 of 780 (70.00%): 854664.262256 marker*pairs/sec - -0.017976 sec at pair 624 of 780 (80.00%): 867821.563192 marker*pairs/sec - -0.020017 sec at pair 702 of 780 (90.00%): 876748.317016 marker*pairs/sec - -T1: 0.00267601013184 T2: 0.0181350708008 T3: 0.000470638275146 TOT: 0.0224170684814 0 pairs with no (or not enough) comparable genotypes (0.0%) +T1: 0.00229454040527 T2: 0.0166795253754 T3: 0.000442743301392 TOT: 0.0201091766357 0 pairs with no (or not enough) comparable genotypes (0.0%) Relstate dupe: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00 -Relstate parentchild: mean(mean)=1.68 sdev(mean)=0.19, mean(sdev)=0.39 sdev(sdev)=0.19 +Relstate parentchild: mean(mean)=1.82 sdev(mean)=0.14, mean(sdev)=0.33 sdev(sdev)=0.22 Relstate sibpairs: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00 Relstate halfsibs: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00 -Relstate parents: mean(mean)=1.46 sdev(mean)=0.25, mean(sdev)=0.55 sdev(sdev)=0.17 +Relstate parents: mean(mean)=1.62 sdev(mean)=0.21, mean(sdev)=0.53 sdev(sdev)=0.29 -Relstate unrelated: mean(mean)=1.44 sdev(mean)=0.21, mean(sdev)=0.58 sdev(sdev)=0.15 +Relstate unrelated: mean(mean)=1.60 sdev(mean)=0.23, mean(sdev)=0.54 sdev(sdev)=0.22 Relstate unknown: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00 diff -r ed5535c4d48e -r 92ce16e0e37e test-data/rgtestouts/rgGRR/rgGRRtest1.svg --- a/test-data/rgtestouts/rgGRR/rgGRRtest1.svg Thu Apr 15 15:58:08 2010 -0400 +++ b/test-data/rgtestouts/rgGRR/rgGRRtest1.svg Thu Apr 15 21:20:04 2010 -0400 @@ -5,9 +5,9 @@ xmlns="http://www.w3.org/2000/svg" version="1.2" xmlns:xlink="http://www.w3.org/1999/xlink" viewBox="0 0 1280 800" onload="init()"> - <script type="text/ecmascript" xlink:href="/static/scripts/tools/rgenetics/checkbox_and_radiobutton.js"/> - <script type="text/ecmascript" xlink:href="/static/scripts/tools/rgenetics/helper_functions.js"/> - <script type="text/ecmascript" xlink:href="/static/scripts/tools/rgenetics/timer.js"/> + <script type="text/ecmascript" xlink:href="/static/scripts/checkbox_and_radiobutton.js"/> + <script type="text/ecmascript" xlink:href="/static/scripts/helper_functions.js"/> + <script type="text/ecmascript" xlink:href="/static/scripts/timer.js"/> <script type="text/ecmascript"> <![CDATA[ var checkBoxes = new Array(); @@ -247,492 +247,99 @@  <g style="fill:black; stroke:none" font-size="18" font-family="Arial"> - <text x="425" y="-30">rgGRRtest1 (40 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+rs16823529 1 3161070 1.000 0.000000 0.534 0.272621 0.541 0.266883 1.000 0.000000 +rs12075867 1 3161113 1.000 0.000000 0.191 0.719422 0.193 0.713768 1.000 0.000000 +rs2817148 1 3161293 1.000 0.000000 0.009 2.050269 0.006 2.244583 1.000 0.000000 +rs2651891 1 3163073 1.000 0.000000 0.009 2.050269 0.006 2.244583 1.000 0.000000 +rs16823551 1 3164773 1.000 0.000000 0.005 2.260982 0.004 2.447453 1.000 0.000000 +rs10157420 1 3169654 1.000 0.000000 0.413 0.383840 0.432 0.364919 1.000 0.000000 +rs6424069 1 3170187 1.000 0.000000 0.004 2.354381 0.003 2.495257 1.000 0.000000 + diff -r ed5535c4d48e -r 92ce16e0e37e tools/rgenetics/rgGLM.xml --- a/tools/rgenetics/rgGLM.xml Thu Apr 15 15:58:08 2010 -0400 +++ b/tools/rgenetics/rgGLM.xml Thu Apr 15 21:20:04 2010 -0400 @@ -68,7 +68,7 @@ <param name='maf' value='0.0' /> <param name='logistic' value='0' /> <output name='out_file1' file='rgGLMtest1_GLM.xls' ftype='tabular' compare="diff" /> - <output name='logf' file='rgGLMtest1_GLM_log.txt' ftype='txt' compare="diff" lines_diff='33'/> + <output name='logf' file='rgGLMtest1_GLM_log.txt' ftype='txt' compare="diff" lines_diff='36'/> <output name='gffout' file='rgGLMtest1_GLM_topTable.gff' compare="diff" ftype='gff' /> </test> </tests> diff -r ed5535c4d48e -r 92ce16e0e37e tools/rgenetics/rgGRR.py --- a/tools/rgenetics/rgGRR.py Thu Apr 15 15:58:08 2010 -0400 +++ b/tools/rgenetics/rgGRR.py Thu Apr 15 21:20:04 2010 -0400 @@ -639,7 +639,7 @@ skip = set() ndone = 0 ## How many have been done so far - logf.write('Calculating %d pairs, updating every %d pairs...\n' % (tot, nprog)) + logf.write('Calculating %d pairs...\n' % (tot)) logf.write('Estimated time is %2.2f to %2.2f seconds ...\n' % (estimatedTimeFast, estimatedTimeSlow)) t1sum = 0 @@ -695,10 +695,6 @@ for s2 in xrange(s1+1, nSubjects): if s2 in emptyRows: continue - if nprog and ndone % nprog == 0 and ndone > 1: - dur = time.time() - started - pct = float(ndone)/tot*100.0 - logf.write('%f sec at pair %d of %d (%3.2f%%): %f marker*pairs/sec\n' % (dur, ndone, tot, pct, ndone/dur*nrsSamples)) t1s = time.time() (fid2,iid2,did2,mid2,sex2,phe2,iid2,d_sid2,m_sid2) = scache.setdefault(s2, ped.getSubject(s2)) @@ -848,9 +844,7 @@ continue outliers = [(scalefactor*int(abs(x[3]))+ int(abs(x[2])),x) for x in outliers] # decorate outliers.sort() - logf.write('### outliers after decorated sort=%s' % outliers) outliers.reverse() # largest deviation first - logf.write('### outliers after decorated sort=%s' % outliers) outliers = [x[1] for x in outliers] # undecorate nrows = len(outliers) truncated = 0 diff -r ed5535c4d48e -r 92ce16e0e37e tools/rgenetics/rgGRR.xml --- a/tools/rgenetics/rgGRR.xml Thu Apr 15 15:58:08 2010 -0400 +++ b/tools/rgenetics/rgGRR.xml Thu Apr 15 21:20:04 2010 -0400 @@ -29,7 +29,7 @@ <param name='n' value='100' /> <param name='Z' value='6' /> <output name='out_file1' file='rgtestouts/rgGRR/rgGRRtest1.html' ftype='html' compare="diff" lines_diff='30'> - <extra_files type="file" name='Log_rgGRRtest1.txt' value="rgtestouts/rgGRR/Log_rgGRRtest1.txt" compare="diff" lines_diff="30"/> + <extra_files type="file" name='Log_rgGRRtest1.txt' value="rgtestouts/rgGRR/Log_rgGRRtest1.txt" compare="diff" lines_diff="70"/> <extra_files type="file" name='rgGRRtest1.svg' value="rgtestouts/rgGRR/rgGRRtest1.svg" compare="diff" lines_diff="1000" /> <extra_files type="file" name='rgGRRtest1_table.xls' value="rgtestouts/rgGRR/rgGRRtest1_table.xls" compare="diff" lines_diff="100" /> </output> diff -r ed5535c4d48e -r 92ce16e0e37e tools/rgenetics/rgQC.xml --- a/tools/rgenetics/rgQC.xml Thu Apr 15 15:58:08 2010 -0400 +++ b/tools/rgenetics/rgQC.xml Thu Apr 15 21:20:04 2010 -0400 @@ -27,7 +27,7 @@ <composite_data value='tinywga.fam' /> </param> <param name='out_prefix' value='rgQCtest1' /> - <output name='html_file' file='rgtestouts/rgQC/rgQCtest1.html' ftype='html' lines_diff='250'> + <output name='html_file' file='rgtestouts/rgQC/rgQCtest1.html' ftype='html' lines_diff='260'> <extra_files type="file" name='tinywga_All_Paged.pdf' value="rgtestouts/rgQC/tinywga_All_Paged.pdf" compare="diff" lines_diff="2600"/> <extra_files type="file" name='tinywga.log' value="rgtestouts/rgQC/tinywga.log" compare="diff" lines_diff="10"/> <extra_files type="file" name='tinywga.frq' value="rgtestouts/rgQC/tinywga.frq" compare="diff" />

1 0

[hg] galaxy 3660: Decouple the Galaxy specific foms stuff ( addr...
by Greg Von Kuster 15 Apr '10

15 Apr '10

details: http://www.bx.psu.edu/hg/galaxy/rev/ed5535c4d48e changeset: 3660:ed5535c4d48e user: Greg Von Kuster <greg(a)bx.psu.edu> date: Thu Apr 15 15:58:08 2010 -0400 description: Decouple the Galaxy specific foms stuff ( address, etc ) from the User Preferences page. diffstat: lib/galaxy/web/controllers/user.py | 122 ++++++++++------- templates/user/index.mako | 6 +- templates/user/info.mako | 207 ++++++---------------------- templates/webapps/community/user/info.mako | 9 + templates/webapps/galaxy/user/info.mako | 122 +++++++++++++++++ 5 files changed, 252 insertions(+), 214 deletions(-) diffs (651 lines): diff -r 1dc7e6c15272 -r ed5535c4d48e lib/galaxy/web/controllers/user.py --- a/lib/galaxy/web/controllers/user.py Thu Apr 15 12:33:28 2010 -0400 +++ b/lib/galaxy/web/controllers/user.py Thu Apr 15 15:58:08 2010 -0400 @@ -297,6 +297,8 @@ def __validate_username( self, trans, username, user=None ): # User names must be at least four characters in length and contain only lower-case # letters, numbers, and the '-' character. + if username in [ 'None', None, '' ]: + return None if user and user.username == username: return None if len( username ) < 4: @@ -323,17 +325,14 @@ error = self.__validate_username( trans, username ) if not error: if webapp == 'galaxy': - # TODO: the user controller must be decoupled from the model, so this import causes problems. - # The get_all_forms method is used only if Galaxy is the webapp, so it needs to be re-worked - # so that it can be imported with no problems if the controller is not 'galaxy'. from galaxy.web.controllers.forms import get_all_forms if len( get_all_forms( trans, filter=dict( deleted=False ), form_type=trans.app.model.FormDefinition.types.USER_INFO ) ): if not params.get( 'user_info_select', False ): - return 'Select the user type and the user information' + return "Select the user's type and information" return error - def __user_info_ui(self, trans, user=None, **kwd): + def __user_info_ui( self, trans, user=None, **kwd ): ''' This method creates the user type select box & user information form widgets and is called during user registration and editing user information. @@ -342,14 +341,12 @@ show a selectbox containing all the forms, then the user can select the one that fits the user's description the most ''' - # TODO: the user controller must be decoupled from the model, so this import causes problems. - # The get_all_forms method is used only if Galaxy is the webapp, so it needs to be re-worked - # so that it can be imported with no problems if the controller is not 'galaxy'. from galaxy.web.controllers.forms import get_all_forms params = util.Params( kwd ) # get all the user information forms - user_info_forms = get_all_forms( trans, filter=dict(deleted=False), - form_type=trans.app.model.FormDefinition.types.USER_INFO ) + user_info_forms = get_all_forms( trans, + filter=dict( deleted=False ), + form_type=trans.app.model.FormDefinition.types.USER_INFO ) user_info_select = None if user: if user.values: @@ -398,19 +395,15 @@ information, public user name, reset password & other user information obtained during registration ''' - # TODO: the user controller must be decoupled from the model, so this import causes problems. - # The get_all_forms method is used only if Galaxy is the webapp, so it needs to be re-worked - # so that it can be imported with no problems if the controller is not 'galaxy'. - from galaxy.web.controllers.forms import get_all_forms params = util.Params( kwd ) user_id = params.get( 'user_id', None ) + webapp = params.get( 'webapp', 'galaxy' ) if user_id: user = trans.sa_session.query( trans.app.model.User ).get( int( user_id ) ) else: user = trans.user if not user: - # TODO: handle this without the deprecated exception. - raise "In show_info, we don't have a valid user" + raise AssertionError, "The user id (%s) is not valid" % str( user_id ) email = util.restore_text( params.get( 'email', user.email ) ) # Do not sanitize passwords, so take from kwd # instead of params ( which were sanitized ) @@ -423,38 +416,55 @@ admin_view = util.string_as_bool( params.get( 'admin_view', False ) ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - user_info_select, user_info_form, widgets = self.__user_info_ui( trans, user, **kwd ) - # user's addresses - show_filter = util.restore_text( params.get( 'show_filter', 'Active' ) ) - if show_filter == 'All': - addresses = [address for address in user.addresses] - elif show_filter == 'Deleted': - addresses = [address for address in user.addresses if address.deleted] + if webapp == 'galaxy': + from galaxy.web.controllers.forms import get_all_forms + user_info_select, user_info_form, widgets = self.__user_info_ui( trans, user, **kwd ) + # user's addresses + show_filter = util.restore_text( params.get( 'show_filter', 'Active' ) ) + if show_filter == 'All': + addresses = [address for address in user.addresses] + elif show_filter == 'Deleted': + addresses = [address for address in user.addresses if address.deleted] + else: + addresses = [address for address in user.addresses if not address.deleted] + user_info_forms = get_all_forms( trans, + filter=dict( deleted=False ), + form_type=trans.app.model.FormDefinition.types.USER_INFO ) + return trans.fill_template( '/webapps/galaxy/user/info.mako', + user=user, + email=email, + current=current, + password=password, + confirm=confirm, + username=username, + user_info_select=user_info_select, + user_info_forms=user_info_forms, + user_info_form=user_info_form, + widgets=widgets, + addresses=addresses, + show_filter=show_filter, + admin_view=admin_view, + webapp=webapp, + message=message, + status=status ) else: - addresses = [address for address in user.addresses if not address.deleted] - user_info_forms = get_all_forms( trans, filter=dict(deleted=False), - form_type=trans.app.model.FormDefinition.types.USER_INFO ) - return trans.fill_template( '/user/info.mako', - user=user, - email=email, - current=current, - password=password, - confirm=confirm, - username=username, - user_info_select=user_info_select, - user_info_forms=user_info_forms, - user_info_form=user_info_form, - widgets=widgets, - addresses=addresses, - show_filter=show_filter, - admin_view=admin_view, - message=message, - status=status ) + return trans.fill_template( '/webapps/community/user/info.mako', + user=user, + email=email, + current=current, + password=password, + confirm=confirm, + username=username, + admin_view=False, + webapp=webapp, + message=message, + status=status ) @web.expose def edit_info( self, trans, **kwd ): params = util.Params( kwd ) user_id = params.get( 'user_id', None ) admin_view = util.string_as_bool( params.get( 'admin_view', False ) ) + webapp = params.get( 'webapp', 'galaxy' ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) if user_id: @@ -467,11 +477,12 @@ username = util.restore_text( params.get( 'username', '' ) ).lower() # validate the new values error = self.__validate_email( trans, email, user ) - if not error: + if not error and username: error = self.__validate_username( trans, username, user ) if error: return trans.response.send_redirect( web.url_for( controller='user', action='show_info', + webapp=webapp, message=error, status='error') ) # The user's private role name must match the user's login ( email ) @@ -484,15 +495,17 @@ trans.sa_session.add_all( ( user, private_role ) ) trans.sa_session.flush() message = 'The login information has been updated with the changes' - if admin_view: + if webapp == 'galaxy' and admin_view: return trans.response.send_redirect( web.url_for( controller='user', action='show_info', user_id=user.id, admin_view=admin_view, + webapp=webapp, message=message, status='done' ) ) return trans.response.send_redirect( web.url_for( controller='user', action='show_info', + webapp=webapp, message=message, status='done') ) # Change password @@ -502,27 +515,30 @@ password = kwd.get( 'password', '' ) confirm = kwd.get( 'confirm', '' ) # When from the user perspective, validate the current password - if not admin_view: + if not webapp == 'galaxy' and not admin_view: # Do not sanitize passwords, so get from kwd and not params # ( which were sanitized ). current = kwd.get( 'current', '' ) if not trans.user.check_password( current ): return trans.response.send_redirect( web.url_for( controller='user', action='show_info', + webapp=webapp, message='Invalid current password', status='error') ) # validate the new values error = self.__validate_password( trans, password, confirm ) if error: - if admin_view: + if webapp == 'galaxy' and admin_view: return trans.response.send_redirect( web.url_for( controller='user', action='show_info', + webapp=webapp, user_id=user.id, admin_view=admin_view, message=error, status='error' ) ) return trans.response.send_redirect( web.url_for( controller='user', action='show_info', + webapp=webapp, message=error, status='error') ) # save new password @@ -531,40 +547,46 @@ trans.sa_session.flush() trans.log_event( "User change password" ) message = 'The password has been changed.' - if admin_view: + if webapp == 'galaxy' and admin_view: return trans.response.send_redirect( web.url_for( controller='user', action='show_info', + webapp=webapp, user_id=user.id, admin_view=admin_view, message=message, status='done' ) ) return trans.response.send_redirect( web.url_for( controller='user', action='show_info', + webapp=webapp, message=message, status='done') ) - # Edit user information + # Edit user information - webapp MUST BE 'galaxy' elif params.get( 'edit_user_info_button', False ): self.__save_user_info(trans, user, "show_info", new_user=False, **kwd) message = "The user information has been updated with the changes." if admin_view: return trans.response.send_redirect( web.url_for( controller='user', action='show_info', + webapp=webapp, user_id=user.id, admin_view=admin_view, message=message, status='done' ) ) return trans.response.send_redirect( web.url_for( controller='user', action='show_info', + webapp=webapp, message=message, status='done') ) else: - if admin_view: + if webapp == 'galaxy' and admin_view: return trans.response.send_redirect( web.url_for( controller='user', action='show_info', + webapp=webapp, user_id=user.id, admin_view=admin_view ) ) return trans.response.send_redirect( web.url_for( controller='user', - action='show_info' ) ) + action='show_info', + webapp=webapp ) ) @web.expose def reset_password( self, trans, email=None, webapp='galaxy', **kwd ): message = util.restore_text( kwd.get( 'message', '' ) ) diff -r 1dc7e6c15272 -r ed5535c4d48e templates/user/index.mako --- a/templates/user/index.mako Thu Apr 15 12:33:28 2010 -0400 +++ b/templates/user/index.mako Thu Apr 15 15:58:08 2010 -0400 @@ -10,8 +10,10 @@ <p>You are currently logged in as ${trans.user.email}.</p> <ul> %if webapp == 'galaxy': - <li><a href="${h.url_for( action='show_info' )}">${_('Manage your information')}</a></li> - <li><a href="${h.url_for( action='set_default_permissions' )}">${_('Change default permissions')}</a> for new histories</li> + <li><a href="${h.url_for( controller='user', action='show_info' )}">${_('Manage your information')}</a></li> + <li><a href="${h.url_for( controller='user', action='set_default_permissions' )}">${_('Change default permissions')}</a> for new histories</li> + %else: + <li><a href="${h.url_for( controller='user', action='show_info', webapp='community' )}">${_('Manage your information')}</a></li> %endif </ul> %else: diff -r 1dc7e6c15272 -r ed5535c4d48e templates/user/info.mako --- a/templates/user/info.mako Thu Apr 15 12:33:28 2010 -0400 +++ b/templates/user/info.mako Thu Apr 15 15:58:08 2010 -0400 @@ -1,176 +1,59 @@ <%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> -%if message: - ${render_msg( message, status )} -%endif - -<h2>Manage User Information</h2> -%if not admin_view: - <ul class="manage-table-actions"> - <li> - <a class="action-button" href="${h.url_for( controller='user', action='index')}"> - <span>User preferences</span></a> - </li> - </ul> -%endif - -<script type="text/javascript"> -$( function() { - $( "select[refresh_on_change='true']").change( function() { - var refresh = false; - var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' ) - if ( refresh_on_change_values ) { - refresh_on_change_values = refresh_on_change_values.value.split( ',' ); - var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' ); - for( i= 0; i < refresh_on_change_values.length; i++ ) { - if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){ - refresh = true; - break; - } - } - } - else { - refresh = true; - } - if ( refresh ){ - $( "#user_info" ).submit(); - } - }); -}); -</script> - -<div class="toolForm"> - <form name="login_info" id="login_info" action="${h.url_for( controller='user', action='edit_info', user_id=user.id, admin_view=admin_view )}" method="post" > - <div class="toolFormTitle">Login Information</div> - <div class="form-row"> - <label>Email address:</label> - <input type="text" name="email" value="${email}" size="40"/> - </div> - <div class="form-row"> - <label>Public user name:</label> - <input type="text" name="username" size="40" value="${username}"/> - <div class="toolParamHelp" style="clear: both;"> - Your user name is an optional identifier that will be used to generate addresses for information - you share publicly. User names must be at least four characters in length and contain only lower-case - letters, numbers, and the '-' character. +<%def name="render_user_info()"> + <h2>Manage User Information</h2> + %if not admin_view: + <ul class="manage-table-actions"> + <li> + <a class="action-button" href="${h.url_for( controller='user', action='index' )}"> + <span>User preferences</span></a> + </li> + </ul> + %endif + <div class="toolForm"> + <form name="login_info" id="login_info" action="${h.url_for( controller='user', action='edit_info', user_id=user.id, admin_view=admin_view )}" method="post" > + <div class="toolFormTitle">Login Information</div> + <div class="form-row"> + <label>Email address:</label> + <input type="text" name="email" value="${email}" size="40"/> </div> - </div> - <div class="form-row"> - <input type="submit" name="login_info_button" value="Save"/> - </div> - </form> -</div> -<p></p> -<div class="toolForm"> - <form name="change_password" id="change_password" action="${h.url_for( controller='user', action='edit_info', user_id=user.id, admin_view=admin_view )}" method="post" > - <div class="toolFormTitle">Change Password</div> - %if not admin_view: <div class="form-row"> - <label>Current Password:</label> - <input type="password" name="current" value="${current}" size="40"/> + <label>Public user name:</label> + <input type="text" name="username" size="40" value="${username}"/> + <div class="toolParamHelp" style="clear: both;"> + Your user name is an optional identifier that will be used to generate addresses for information + you share publicly. User names must be at least four characters in length and contain only lower-case + letters, numbers, and the '-' character. + </div> </div> - %endif - <div class="form-row"> - <label>New Password:</label> - <input type="password" name="password" value="${password}" size="40"/> - </div> - <div class="form-row"> - <label>Confirm:</label> - <input type="password" name="confirm" value="${confirm}" size="40"/> - </div> - <div class="form-row"> - <input type="submit" name="change_password_button" value="Save"/> - </div> - </form> -</div> -%if user.values or user_info_forms: - <p></p> - <div class="toolForm"> - <form name="user_info" id="user_info" action="${h.url_for( controller='user', action='edit_info', user_id=user.id, admin_view=admin_view )}" method="post" > - <div class="toolFormTitle">User information</div> - %if user_info_select: - <div class="form-row"> - <label>User type:</label> - ${user_info_select.get_html()} - </div> - %endif - - %for field in widgets: - <div class="form-row"> - <label>${field['label']}:</label> - ${field['widget'].get_html()} - <div class="toolParamHelp" style="clear: both;"> - ${field['helptext']} - </div> - <div style="clear: both"></div> - </div> - %endfor - %if not user_info_select: - <input type="hidden" name="user_info_select" value="${user_info_form.id}"/> - %endif - <div class="form-row"> - <input type="submit" name="edit_user_info_button" value="Save"/> + <input type="hidden" name="webapp" value="${webapp}" size="40"/> + <input type="submit" name="login_info_button" value="Save"/> </div> </form> </div> -%endif -<p></p> -<div class="toolForm"> - <form name="user_info" id="user_info" action="${h.url_for( controller='user', action='new_address', user_id=user.id, admin_view=admin_view )}" method="post" > - <div class="toolFormTitle">User Addresses</div> - <div class="toolFormBody"> - %if user.addresses: + <p></p> + <div class="toolForm"> + <form name="change_password" id="change_password" action="${h.url_for( controller='user', action='edit_info', user_id=user.id, admin_view=admin_view )}" method="post" > + <div class="toolFormTitle">Change Password</div> + %if not admin_view: <div class="form-row"> - <div class="grid-header"> - ##<span class="title">Filter:</span> - %for i, filter in enumerate( ['Active', 'Deleted', 'All'] ): - %if i > 0: - <span>|</span> - %endif - %if show_filter == filter: - <span class="filter"><a href="${h.url_for( controller='user', action='show_info', show_filter=filter, user_id=user.id, admin_view=admin_view )}"><b>${filter}</b></a></span> - %else: - <span class="filter"><a href="${h.url_for( controller='user', action='show_info', show_filter=filter, user_id=user.id, admin_view=admin_view )}">${filter}</a></span> - %endif - %endfor + <label>Current Password:</label> + <input type="password" name="current" value="${current}" size="40"/> </div> - </div> - <table class="grid"> - <tbody> - %for index, address in enumerate(addresses): - <tr class="libraryRow libraryOrFolderRow" id="libraryRow"> - <td> - <div class="form-row"> - <label>${address.desc}:</label> - ${address.get_html()} - </div> - <div class="form-row"> - <ul class="manage-table-actions"> - <li> - %if not address.deleted: - <a class="action-button" href="${h.url_for( controller='user', action='edit_address', admin_view=admin_view, address_id=address.id, user_id=user.id )}"> - <span>Edit</span></a> - <a class="action-button" href="${h.url_for( controller='user', action='delete_address', admin_view=admin_view, address_id=address.id, user_id=user.id)}"> - <span>Delete</span></a> - %else: - <a class="action-button" href="${h.url_for( controller='user', action='undelete_address', admin_view=admin_view, address_id=address.id, user_id=user.id)}"> - <span>Undelete</span></a> - %endif - - </li> - </ul> - </div> - </td> - </tr> - %endfor - </tbody> - </table> %endif <div class="form-row"> - <input type="submit" value="Add a new address"> + <label>New Password:</label> + <input type="password" name="password" value="${password}" size="40"/> </div> - </div> - </form> -</div> + <div class="form-row"> + <label>Confirm:</label> + <input type="password" name="confirm" value="${confirm}" size="40"/> + </div> + <div class="form-row"> + <input type="hidden" name="webapp" value="${webapp}" size="40"/> + <input type="submit" name="change_password_button" value="Save"/> + </div> + </form> + </div> +</%def> diff -r 1dc7e6c15272 -r ed5535c4d48e templates/webapps/community/user/info.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/webapps/community/user/info.mako Thu Apr 15 15:58:08 2010 -0400 @@ -0,0 +1,9 @@ +<%inherit file="/base.mako"/> +<%namespace file="/user/info.mako" import="render_user_info" /> +<%namespace file="/message.mako" import="render_msg" /> + +%if message: + ${render_msg( message, status )} +%endif + +${render_user_info()} diff -r 1dc7e6c15272 -r ed5535c4d48e templates/webapps/galaxy/user/info.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/webapps/galaxy/user/info.mako Thu Apr 15 15:58:08 2010 -0400 @@ -0,0 +1,122 @@ +<%inherit file="/base.mako"/> +<%namespace file="/user/info.mako" import="render_user_info" /> +<%namespace file="/message.mako" import="render_msg" /> + +<script type="text/javascript"> +$( function() { + $( "select[refresh_on_change='true']").change( function() { + var refresh = false; + var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' ) + if ( refresh_on_change_values ) { + refresh_on_change_values = refresh_on_change_values.value.split( ',' ); + var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' ); + for( i= 0; i < refresh_on_change_values.length; i++ ) { + if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){ + refresh = true; + break; + } + } + } + else { + refresh = true; + } + if ( refresh ){ + $( "#user_info" ).submit(); + } + }); +}); +</script> + +%if message: + ${render_msg( message, status )} +%endif + +${render_user_info()} + +%if user.values or user_info_forms: + <p></p> + <div class="toolForm"> + <form name="user_info" id="user_info" action="${h.url_for( controller='user', action='edit_info', user_id=user.id, admin_view=admin_view )}" method="post" > + <div class="toolFormTitle">User information</div> + %if user_info_select: + <div class="form-row"> + <label>User type:</label> + ${user_info_select.get_html()} + </div> + %endif + %for field in widgets: + <div class="form-row"> + <label>${field['label']}:</label> + ${field['widget'].get_html()} + <div class="toolParamHelp" style="clear: both;"> + ${field['helptext']} + </div> + <div style="clear: both"></div> + </div> + %endfor + %if not user_info_select: + <input type="hidden" name="user_info_select" value="${user_info_form.id}"/> + %endif + + <div class="form-row"> + <input type="submit" name="edit_user_info_button" value="Save"/> + </div> + </form> + </div> + <p></p> +%endif + +<div class="toolForm"> + <p></p> + <form name="user_info" id="user_info" action="${h.url_for( controller='user', action='new_address', user_id=user.id, admin_view=admin_view )}" method="post" > + <div class="toolFormTitle">User Addresses</div> + <div class="toolFormBody"> + %if user.addresses: + <div class="form-row"> + <div class="grid-header"> + %for i, filter in enumerate( ['Active', 'Deleted', 'All'] ): + %if i > 0: + <span>|</span> + %endif + %if show_filter == filter: + <span class="filter"><a href="${h.url_for( controller='user', action='show_info', show_filter=filter, user_id=user.id, admin_view=admin_view )}"><b>${filter}</b></a></span> + %else: + <span class="filter"><a href="${h.url_for( controller='user', action='show_info', show_filter=filter, user_id=user.id, admin_view=admin_view )}">${filter}</a></span> + %endif + %endfor + </div> + </div> + <table class="grid"> + <tbody> + %for index, address in enumerate(addresses): + <tr class="libraryRow libraryOrFolderRow" id="libraryRow"> + <td> + <div class="form-row"> + <label>${address.desc}:</label> + ${address.get_html()} + </div> + <div class="form-row"> + <ul class="manage-table-actions"> + <li> + %if not address.deleted: + <a class="action-button" href="${h.url_for( controller='user', action='edit_address', admin_view=admin_view, address_id=address.id, user_id=user.id )}"><span>Edit</span></a> + <a class="action-button" href="${h.url_for( controller='user', action='delete_address', admin_view=admin_view, address_id=address.id, user_id=user.id)}"><span>Delete</span></a> + %else: + <a class="action-button" href="${h.url_for( controller='user', action='undelete_address', admin_view=admin_view, address_id=address.id, user_id=user.id)}"><span>Undelete</span></a> + %endif + </li> + </ul> + </div> + </td> + </tr> + %endfor + </tbody> + </table> + %endif + <div class="form-row"> + <input type="submit" value="Add a new address"> + </div> + </div> + </form> + <p></p> +</div>

1 0

[hg] galaxy 3659: Have fastq set_meta() only skip counting 'comm...
by Greg Von Kuster 15 Apr '10

15 Apr '10

details: http://www.bx.psu.edu/hg/galaxy/rev/1dc7e6c15272 changeset: 3659:1dc7e6c15272 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Thu Apr 15 12:33:28 2010 -0400 description: Have fastq set_meta() only skip counting 'comment lines' when they are before any sequences. This is still not properly determining sequence counts in cases where line wrapping occurs; quality score lines can start with e.g. '#' and '@'. diffstat: lib/galaxy/datatypes/sequence.py | 2 +- 1 files changed, 1 insertions(+), 1 deletions(-) diffs (12 lines): diff -r df40eae8e86b -r 1dc7e6c15272 lib/galaxy/datatypes/sequence.py --- a/lib/galaxy/datatypes/sequence.py Thu Apr 15 11:10:57 2010 -0400 +++ b/lib/galaxy/datatypes/sequence.py Thu Apr 15 12:33:28 2010 -0400 @@ -163,7 +163,7 @@ seq_counter = 0 # blocks should be 4 lines long for line in file( dataset.file_name ): line = line.strip() - if line and line.startswith( '#' ): + if line and line.startswith( '#' ) and not sequences: # We don't count comment lines for sequence data types continue if line and line.startswith( '@' ):

1 0

[hg] galaxy 3658: changes to help text
by Greg Von Kuster 15 Apr '10

15 Apr '10

details: http://www.bx.psu.edu/hg/galaxy/rev/df40eae8e86b changeset: 3658:df40eae8e86b user: Anton Nekrutenko <anton(a)bx.psu.edu> date: Thu Apr 15 11:10:57 2010 -0400 description: changes to help text diffstat: tools/samtools/pileup_parser.xml | 10 +++++----- 1 files changed, 5 insertions(+), 5 deletions(-) diffs (48 lines): diff -r 33eab99a2df5 -r df40eae8e86b tools/samtools/pileup_parser.xml --- a/tools/samtools/pileup_parser.xml Thu Apr 15 10:51:51 2010 -0400 +++ b/tools/samtools/pileup_parser.xml Thu Apr 15 11:10:57 2010 -0400 @@ -93,7 +93,7 @@ <param name="type_select" value="ten"/> <param name="qv_cutoff" value="20" /> <param name="cvrg_cutoff" value="3" /> - <param name="snps_only" value="Yes"/> + <param name="snps_only" value="Yes"/>q <param name="interval" value="Yes" /> <param name="diff" value="No" /> <param name="qc_base" value="Yes" /> @@ -183,7 +183,7 @@ 2 Position (1-based) 3 Reference base at that position 4 Coverage (# reads aligning over that position) - 5 Bases within reads where (see Galaxy wiki for more info) + 5 Bases within reads 6 Quality values (phred33 scale, see Galaxy wiki for more) **Ten column pileup** @@ -210,7 +210,7 @@ 6 SNP quality 7 Maximum mapping quality 8 Coverage (# reads aligning over that position) - 9 Bases within reads where (see Galaxy wiki for more info) + 9 Bases within reads 10 Quality values (phred33 scale, see Galaxy wiki for more) @@ -255,7 +255,7 @@ 2 Position (1-based) 3 Reference base at that position 4 Coverage (# reads aligning over that position) - 5 Bases within reads where (see Galaxy wiki for more info) + 5 Bases within reads where 6 Quality values (phred33 scale, see Galaxy wiki for more) 7 Number of A variants 8 Number of C variants @@ -289,7 +289,7 @@ 3 End position (1-based) 4 Reference base at that position 5 Coverage (# reads aligning over that position) - 6 Bases within reads where (see Galaxy wiki for more info) + 6 Bases within reads 7 Quality values (phred33 scale, see Galaxy wiki for more) 8 Number of A variants 9 Number of C variants

1 0

[hg] galaxy 3657: Small fixes to rgGRR and rgManQQ
by Greg Von Kuster 15 Apr '10

15 Apr '10

details: http://www.bx.psu.edu/hg/galaxy/rev/33eab99a2df5 changeset: 3657:33eab99a2df5 user: fubar: ross Lazarus at gmail period com date: Thu Apr 15 10:51:51 2010 -0400 description: Small fixes to rgGRR and rgManQQ Prevent default base_name overwriting real base_name in root.py Revert to prevent infotrack being requested - even the latest release of Haploview 4.2 is busted and fails to create any images when creating the infotrack - this only happens in headless mode and seems to be an upstream bug in a java library. No sign of a fix despite multiple pleas to the Haploview authors... Allow https in ucsc genome graphs - suggestion from Assaf Gordon - thanks. Fixes to creation of html page for rgenetics composite datatypes related to base_name problems traced to root.py when user tries to autodetect on the metadata edit page diffstat: lib/galaxy/web/controllers/root.py | 2 +- test-data/rgtestouts/rgManQQ/Allelep_manhattan.png | 0 test-data/rgtestouts/rgManQQ/Armitagep_manhattan.png | 0 test-data/rgtestouts/rgManQQ/rgManQQtest1.R | 52 ++++++++------ test-data/rgtestouts/rgManQQ/rgManQQtest1.html | 10 +-- tools/rgenetics/rgGRR.py | 66 +----------------- tools/rgenetics/rgHaploView.py | 1 + tools/rgenetics/rgHaploView.xml | 2 +- tools/rgenetics/rgManQQ.py | 14 ++-- tools/rgenetics/rgManQQ.xml | 2 +- tools/rgenetics/rgQC.py | 3 +- tools/rgenetics/rgtest_one_tool.sh | 5 +- tools/rgenetics/rgutils.py | 63 +++++++++++++++++- 13 files changed, 115 insertions(+), 105 deletions(-) diffs (453 lines): diff -r 6f43a97e7908 -r 33eab99a2df5 lib/galaxy/web/controllers/root.py --- a/lib/galaxy/web/controllers/root.py Thu Apr 15 10:35:31 2010 -0400 +++ b/lib/galaxy/web/controllers/root.py Thu Apr 15 10:51:51 2010 -0400 @@ -314,7 +314,7 @@ return trans.show_error_message( "This dataset is currently being used as input or output. You cannot change metadata until the jobs have completed or you have canceled them." ) for name, spec in data.metadata.spec.items(): # We need to be careful about the attributes we are resetting - if name not in [ 'name', 'info', 'dbkey' ]: + if name not in [ 'name', 'info', 'dbkey', 'base_name' ]: if spec.get( 'default' ): setattr( data.metadata, name, spec.unwrap( spec.get( 'default' ) ) ) if trans.app.config.set_metadata_externally: diff -r 6f43a97e7908 -r 33eab99a2df5 test-data/rgtestouts/rgManQQ/Allelep_manhattan.png Binary file test-data/rgtestouts/rgManQQ/Allelep_manhattan.png has changed diff -r 6f43a97e7908 -r 33eab99a2df5 test-data/rgtestouts/rgManQQ/Armitagep_manhattan.png Binary file test-data/rgtestouts/rgManQQ/Armitagep_manhattan.png has changed diff -r 6f43a97e7908 -r 33eab99a2df5 test-data/rgtestouts/rgManQQ/rgManQQtest1.R --- a/test-data/rgtestouts/rgManQQ/rgManQQtest1.R Thu Apr 15 10:35:31 2010 -0400 +++ b/test-data/rgtestouts/rgManQQ/rgManQQtest1.R Thu Apr 15 10:51:51 2010 -0400 @@ -22,7 +22,7 @@ manhattan = function(chrom=NULL,offset=NULL,pvals=NULL, title=NULL, max.y="max", - suggestiveline=0, genomewide=T, size.x.labels=9, size.y.labels=10, annotate=F, SNPlist=NULL,grey=F) { + suggestiveline=0, genomewide=T, size.x.labels=9, size.y.labels=10, annotate=F, SNPlist=NULL,grey=0) { if (annotate & is.null(SNPlist)) stop("You requested annotation but provided no SNPlist!") genomewideline=NULL # was genomewideline=-log10(5e-8) @@ -43,10 +43,8 @@ lastbase=0 chrlist = unique(d$CHR) nchr = length(chrlist) # may be any number? - print(paste('## manhattan got chrlist=',chrlist,'nchr',nchr)) for (x in c(1:nchr)) { i = chrlist[x] # need the chrom number - may not == index - print(paste('## manhattan got chrlist=',chrlist,'nchr',nchr,'x=',x,'i=',i)) if (x == 1) { # first time d[d$CHR==i, ]$pos=d[d$CHR==i, ]$BP } else { @@ -63,8 +61,9 @@ } if (max.y=="max") maxy=ceiling(max(d$logp)) else maxy=max.y - if (maxy<8) maxy=8 - + maxy = max(maxy,1.1*genomewideline) + # if (maxy<8) maxy=8 + # only makes sense if genome wide is assumed - we could have a fine mapping region? if (annotate) d.annotate=d[as.numeric(substr(d$SNP,3,100)) %in% SNPlist, ] plot=qplot(pos,logp,data=d, ylab=expression(-log[10](italic(p))) , colour=factor(CHR)) @@ -76,11 +75,13 @@ plot=plot + opts(title=title) plot=plot+opts( panel.background=theme_blank(), - panel.grid.minor=theme_blank(), axis.text.x=theme_text(size=size.x.labels, colour="grey50"), axis.text.y=theme_text(size=size.y.labels, colour="grey50"), axis.ticks=theme_segment(colour=NA) ) + #plot = plot + opts(panel.grid.y.minor=theme_blank(),panel.grid.y.major=theme_blank()) + #plot = plot + opts(panel.grid.major=theme_blank()) + if (suggestiveline) plot=plot+geom_hline(yintercept=suggestiveline,colour="blue", alpha=I(1/3)) if (genomewideline) plot=plot+geom_hline(yintercept=genomewideline,colour="red") plot @@ -107,44 +108,51 @@ if (spartan) plot=plot+opts(panel.background=theme_rect(col="grey50"), panel.grid.minor=theme_blank()) plot } - - -#rs Chr Offset Genop log10Genop Armitagep log10Armitagep Allelep log10Allelep Domp log10Domp -#rs3094315 1 792429 1.000 0.000000 0.122 0.912574 0.152 0.817871 1.000 0.000000 -# eg for testing -# this function needs column numbers so galaxy tool is easy to drive - rgqqMan = function(infile="/opt/galaxy/test-data/smallwgaP.xls",chromcolumn=2, offsetcolumn=3, pvalscolumns=c(6,8), - title="rgManQQtest1",outprefix="rgManQQtest1") { - d = read.table(infile,head=T,sep=' ') - print(paste('###',length(d[,1]),'values read from',infile,'read - now running plots',sep=' ')) +title="rgManQQtest1",grey=0) { +rawd = read.table(infile,head=T,sep=' ') +dn = names(rawd) +cc = dn[chromcolumn] +oc = dn[offsetcolumn] +nams = c(cc,oc) +plen = length(rawd[,1]) +doreorder=1 +print(paste('###',plen,'values read from',infile,'read - now running plots',sep=' ')) +if (plen > 0) { for (pvalscolumn in pvalscolumns) { if (pvalscolumn > 0) { - cname = names(d)[pvalscolumn] + cname = names(rawd)[pvalscolumn] mytitle = paste('p=',cname,', ',title,sep='') myfname = chartr(' ','_',cname) - myqqplot = qq(d[,pvalscolumn],title=mytitle) + myqqplot = qq(rawd[,pvalscolumn],title=mytitle) print(paste('## qqplot on',cname,'done')) if ((chromcolumn > 0) & (offsetcolumn > 0)) { + if (doreorder) { + rawd = rawd[do.call(order,rawd[nams]),] + # mmmf - suggested by http://onertipaday.blogspot.com/2007/08/sortingordering-dataframe-according… + # in case not yet ordered + doreorder = 0 + } print(paste('## manhattan on',cname,'starting',chromcolumn,offsetcolumn,pvalscolumn)) - mymanplot= manhattan(chrom=d[,chromcolumn],offset=d[,offsetcolumn],pvals=d[,pvalscolumn],title=mytitle) + mymanplot= manhattan(chrom=rawd[,chromcolumn],offset=rawd[,offsetcolumn],pvals=rawd[,pvalscolumn],title=mytitle,grey=grey) print(paste('## manhattan plot on',cname,'done')) ggsave(file=paste(myfname,"manhattan.png",sep='_'),mymanplot,width=11,height=8,dpi=100) } else { print(paste('chrom column =',chromcolumn,'offset column = ',offsetcolumn, - 'Cannot parse - no manhattan plot possible')) + 'so no Manhattan plot - supply both chromosome and offset as numerics for Manhattan plots if required')) } - ggsave(file=paste(myfname,"qqplot.png",sep='_'),myqqplot,w=5,h=5,dpi=100) + ggsave(file=paste(myfname,"qqplot.png",sep='_'),myqqplot,width=8,height=11,dpi=100) } else { print(paste('pvalue column =',pvalscolumn,'Cannot parse it so no plots possible')) } } # for pvalscolumn + } else { print('## Problem - no values available to plot - was there really a chromosome and offset column?') } } rgqqMan() # execute with defaults as substituted -#R script autogenerated by rgenetics/rgutils.py on 25/03/2010 21:01:09 +#R script autogenerated by rgenetics/rgutils.py on 15/04/2010 09:56:14 diff -r 6f43a97e7908 -r 33eab99a2df5 test-data/rgtestouts/rgManQQ/rgManQQtest1.html --- a/test-data/rgtestouts/rgManQQ/rgManQQtest1.html Thu Apr 15 10:35:31 2010 -0400 +++ b/test-data/rgtestouts/rgManQQ/rgManQQtest1.html Thu Apr 15 10:51:51 2010 -0400 @@ -38,24 +38,16 @@ [1] "## manhattan on Armitagep starting 2 3 6" -[1] "## manhattan got chrlist= 1 nchr 1" - -[1] "## manhattan got chrlist= 1 nchr 1 x= 1 i= 1" - [1] "## manhattan plot on Armitagep done" [1] "## qqplot on Allelep done" [1] "## manhattan on Allelep starting 2 3 8" -[1] "## manhattan got chrlist= 1 nchr 1" - -[1] "## manhattan got chrlist= 1 nchr 1 x= 1 i= 1" - [1] "## manhattan plot on Allelep done" </pre> -<h3><a href="http://rgenetics.org">Rgenetics</a> tool rgManQQ.py run at 25/03/2010 21:01:19</h3> +<h3><a href="http://rgenetics.org">Rgenetics</a> tool rgManQQ.py run at 15/04/2010 09:56:23</h3> </div></body></html> diff -r 6f43a97e7908 -r 33eab99a2df5 tools/rgenetics/rgGRR.py --- a/tools/rgenetics/rgGRR.py Thu Apr 15 10:35:31 2010 -0400 +++ b/tools/rgenetics/rgGRR.py Thu Apr 15 10:51:51 2010 -0400 @@ -63,7 +63,8 @@ except NameError: from Sets import Set as set -from rgutils import timenow,pruneLD,plinke +from rgutils import timenow,pruneLD,plinke,openOrMakeLDreduced + import plinkbinJZ @@ -1002,61 +1003,6 @@ svg.close() return newfiles,explanations,repOut -def makeOpenLDR(ldreduced=None,basename=None,newfpath=None,plinke='plink'): - """we stow a thin ldreduced version of the primary file in the files_path for future runs - if none there yet - ugh the --thin option will happily return zero snps if only a few - """ - ped = None - loglines = [] - ldbedname = '%s.bed' % ldreduced - ldpedname = '%s.ped' % ldreduced - bedname = '%s.bed' % basename - pedname = '%s.ped' % basename - ldbedfn = os.path.join(newfpath,ldbedname) - ldpedfn = os.path.join(newfpath,ldpedname) - bedfn = os.path.join(newfpath,bedname) - pedfn = os.path.join(newfpath,pedname) - bmap = os.path.join(newfpath,'%s.bim' % basename) - pmap = os.path.join(newfpath,'%s.map' % basename) - if os.path.exists(ldbedfn): # joy. already done - ped = plinkbinJZ.BPed(os.path.splitext(ldbedfn)[0]) - ped.parse(quick=True) - elif os.path.exists(ldpedfn): # why bother - for completeness I guess - ped = plinkbinJZ.LPed(os.path.splitext(ldbedfn)[0]) - ped.parse() - elif os.path.exists(bedfn): # run ld prune and thin and save these for next time - nsnp = len(open(bmap,'r').readlines()) - if nsnp > 100: # if 9 snps --thin 0.1 will happily return 0 snps - plinktasks = [['--bfile',basename,'--indep-pairwise 50 40 0.2','--out %s' % basename], - ['--bfile',basename,'--extract %s.prune.in --make-bed --out %s_INDEP' % (basename, basename)], - ['--bfile %s_INDEP --thin 0.1 --make-bed --out %s' % (basename,ldreduced)]] - else: # no thin stage - plinktasks = [['--bfile',basename,'--indep-pairwise 50 40 0.2','--out %s' % basename], - ['--bfile',basename,'--extract %s.prune.in --make-bed --out %s' % (basename, ldreduced)]] - # subset of ld independent markers for eigenstrat and other requirements - vclbase = [plinke,'--noweb'] - loglines = pruneLD(plinktasks=plinktasks,cd=newfpath,vclbase = vclbase) - ped = plinkbinJZ.BPed(os.path.splitext(ldbedfn)[0]) - ped.parse(quick=True) - elif pedname and os.path.exists(pedfn): # screw it - return a bed - quicker to process - nsnp = len(open(pmap,'r').readlines()) - if nsnp > 100: - plinktasks = [['--file',basename,'--make-bed','--out',basename], - ['--bfile',basename,'--indep-pairwise 50 40 0.2','--out %s' % basename], - ['--bfile',basename,'--extract %s.prune.in --make-bed --out %s_INDEP' % (basename, basename)], - ['--bfile %s_INDEP --thin 0.1 --recode --out %s' % (bedname,ldreduced),]] - else: # no thin step - plinktasks = [['--file',basename,'--make-bed','--out',basename], - ['--bfile',basename,'--indep-pairwise 50 40 0.2','--out %s' % basename], - ['--bfile',basename,'--extract %s.prune.in --make-bed --out %s' % (basename, ldreduced)]] - - # subset of ld independent markers for eigenstrat and other requirements - vclbase = [plinke,'--noweb'] - loglines = pruneLD(plinktasks=plinktasks,cd=newfpath,vclbase = vclbase) - ped = plinkbinJZ.BPed(os.path.splitext(ldbedfn)[0]) - ped.parse(quick=True) - return ped,loglines - def doIBS(n=100): """parse parameters from galaxy expect 'input pbed path' 'basename' 'outpath' 'title' 'logpath' 'n' @@ -1078,6 +1024,7 @@ ts = '%s%s' % (string.punctuation,string.whitespace) ptran = string.maketrans(ts,'_'*len(ts)) inpath = sys.argv[1] + ldpath = os.path.split(inpath)[0] basename = sys.argv[2] outhtml = sys.argv[3] newfilepath = sys.argv[4] @@ -1095,14 +1042,13 @@ pass logf = file(logpath,'w') efp,ibase_name = os.path.split(inpath) # need to use these for outputs in files_path - ldreduced = '%s_INDEP_THIN' % ibase_name # we store ld reduced and thinned data - ped,loglines = makeOpenLDR(ldreduced=ldreduced,basename=ibase_name,newfpath=efp,plinke=plinke) + ped,loglines = openOrMakeLDreduced(basename,ldpath,plinke) if ped == None: - print >> sys.stderr, '## doIBSpy problem - cannot open %s or %s - cannot run' % (bedname,pedname) + print >> sys.stderr, '## doIBSpy problem - cannot open %s or %s - cannot run' % (ldreduced,basename) sys.exit(1) if len(loglines) > 0: logf.write('### first time for this input file - log from creating an ld reduced and thinned data set:\n') - logf.write('\n'.join(loglines)) + logf.write(''.join(loglines)) logf.write('\n') newfiles,explanations,repOut = doIBSpy(ped=ped,basename=basename,outdir=newfilepath, logf=logf,nrsSamples=n,title=title,pdftoo=0,Zcutoff=Zcutoff) diff -r 6f43a97e7908 -r 33eab99a2df5 tools/rgenetics/rgHaploView.py --- a/tools/rgenetics/rgHaploView.py Thu Apr 15 10:35:31 2010 -0400 +++ b/tools/rgenetics/rgHaploView.py Thu Apr 15 10:51:51 2010 -0400 @@ -84,6 +84,7 @@ outfpath = sys.argv[12] infotrack = False # note that otherwise this breaks haploview in headless mode #infotrack = sys.argv[13] == 'info' + # this fails in headless mode as at april 2010 with haploview 4.2 tagr2 = sys.argv[14] or '0.8' hmpanels = sys.argv[15] # eg "['CEU','YRI']" if hmpanels: diff -r 6f43a97e7908 -r 33eab99a2df5 tools/rgenetics/rgHaploView.xml --- a/tools/rgenetics/rgHaploView.xml Thu Apr 15 10:35:31 2010 -0400 +++ b/tools/rgenetics/rgHaploView.xml Thu Apr 15 10:51:51 2010 -0400 @@ -53,7 +53,7 @@ <param name="infoTrack" type="select" label="Add Hapmap information track to image" help="Refseq genes and snp density can be added to the plot if desired for orientation" > - <option value="info">Add Information track (Not available - awaiting fix from Haploview authors)</option> + <option value="info">Add Information track (DISABLED! Awaiting fix from Haploview authors)</option> <option value="noinfo" selected="True">No Information track</option> </param> diff -r 6f43a97e7908 -r 33eab99a2df5 tools/rgenetics/rgManQQ.py --- a/tools/rgenetics/rgManQQ.py Thu Apr 15 10:35:31 2010 -0400 +++ b/tools/rgenetics/rgManQQ.py Thu Apr 15 10:51:51 2010 -0400 @@ -129,27 +129,27 @@ cc = dn[chromcolumn] oc = dn[offsetcolumn] nams = c(cc,oc) -plen = length(d[,1]) -doreorder=True +plen = length(rawd[,1]) +doreorder=1 print(paste('###',plen,'values read from',infile,'read - now running plots',sep=' ')) if (plen > 0) { for (pvalscolumn in pvalscolumns) { if (pvalscolumn > 0) { - cname = names(d)[pvalscolumn] + cname = names(rawd)[pvalscolumn] mytitle = paste('p=',cname,', ',title,sep='') myfname = chartr(' ','_',cname) - myqqplot = qq(d[,pvalscolumn],title=mytitle) + myqqplot = qq(rawd[,pvalscolumn],title=mytitle) print(paste('## qqplot on',cname,'done')) if ((chromcolumn > 0) & (offsetcolumn > 0)) { if (doreorder) { - d = rawd[do.call(order,rawd[nams]),] + rawd = rawd[do.call(order,rawd[nams]),] # mmmf - suggested by http://onertipaday.blogspot.com/2007/08/sortingordering-dataframe-according… # in case not yet ordered - doreorder = False + doreorder = 0 } print(paste('## manhattan on',cname,'starting',chromcolumn,offsetcolumn,pvalscolumn)) - mymanplot= manhattan(chrom=d[,chromcolumn],offset=d[,offsetcolumn],pvals=d[,pvalscolumn],title=mytitle,grey=grey) + mymanplot= manhattan(chrom=rawd[,chromcolumn],offset=rawd[,offsetcolumn],pvals=rawd[,pvalscolumn],title=mytitle,grey=grey) print(paste('## manhattan plot on',cname,'done')) ggsave(file=paste(myfname,"manhattan.png",sep='_'),mymanplot,width=11,height=8,dpi=100) } diff -r 6f43a97e7908 -r 33eab99a2df5 tools/rgenetics/rgManQQ.xml --- a/tools/rgenetics/rgManQQ.xml Thu Apr 15 10:35:31 2010 -0400 +++ b/tools/rgenetics/rgManQQ.xml Thu Apr 15 10:51:51 2010 -0400 @@ -37,7 +37,7 @@ <test> <param name='i' value='smallwgaP.xls' ftype='tabular' > </param> - <param name='name' value='rgManQQ_test1' /> + <param name='name' value='rgManQQtest1' /> <param name='pval_col' value='5,7' /> <param name='chrom_col' value='1' /> <param name='offset_col' value='2' /> diff -r 6f43a97e7908 -r 33eab99a2df5 tools/rgenetics/rgQC.py --- a/tools/rgenetics/rgQC.py Thu Apr 15 10:35:31 2010 -0400 +++ b/tools/rgenetics/rgQC.py Thu Apr 15 10:51:51 2010 -0400 @@ -1264,8 +1264,7 @@ plinktasks = [['--freq',],['--hwe 0.0', '--missing','--hardy'], ['--mendel',],['--check-sex',]] vclbase = [options.plinke,'--noweb','--out',basename,'--bfile',bfn,'--mind','1.0','--geno','1.0','--maf','0.0'] - runPlink(bfn = bfn,ofn = ofn,logf=plogf,plinktasks=plinktasks,cd=newfpath, - vclbase=vclbase) + runPlink(logf=plogf,plinktasks=plinktasks,cd=newfpath, vclbase=vclbase) plinktasks = [['--bfile',bfn,'--indep-pairwise 40 20 0.5','--out %s' % basename], ['--bfile',bfn,'--extract %s.prune.in --make-bed --out ldp_%s' % (basename, basename)], ['--bfile ldp_%s --het --out %s' % (basename,basename)]] diff -r 6f43a97e7908 -r 33eab99a2df5 tools/rgenetics/rgtest_one_tool.sh --- a/tools/rgenetics/rgtest_one_tool.sh Thu Apr 15 10:35:31 2010 -0400 +++ b/tools/rgenetics/rgtest_one_tool.sh Thu Apr 15 10:51:51 2010 -0400 @@ -6,11 +6,12 @@ *) esac GALAXYROOT=`pwd` +PATHTOGALAXY='/opt/galaxy' # whatever echo "using $GALAXYROOT" # change this as needed for your local install INPATH="${GALAXYROOT}/test-data" BINPATH="${GALAXYROOT}/tool-data/rg/bin" -TOOLPATH="${GALAXYROOT}/tools/rgenetics" +TOOLPATH="${PATHTOGALAXY}/tools/rgenetics" OROOT="${GALAXYROOT}/test-data/rgtestouts" NORMALOROOT="${GALAXYROOT}/test-data" case "$1" in @@ -67,6 +68,8 @@ echo "now doing $TOOL" OUTPATH="$OROOT/$TOOL" rm -rf $OUTPATH/* +cmd="$TOOLPATH/$TOOL.py "$INPATH/tinywga" "tinywga" $OUTPATH/${NPRE}.html $OUTPATH "$NPRE" '100' '6'" +echo "Doing $cmd" python $TOOLPATH/$TOOL.py "$INPATH/tinywga" "tinywga" $OUTPATH/${NPRE}.html $OUTPATH "$NPRE" '100' '6' # rgGRR.py $i.extra_files_path/$i.metadata.base_name "$i.metadata.base_name" #'$out_file1' '$out_file1.files_path' "$title" '$n' '$Z' diff -r 6f43a97e7908 -r 33eab99a2df5 tools/rgenetics/rgutils.py --- a/tools/rgenetics/rgutils.py Thu Apr 15 10:35:31 2010 -0400 +++ b/tools/rgenetics/rgutils.py Thu Apr 15 10:51:51 2010 -0400 @@ -4,7 +4,7 @@ # released under the LGPL # -import subprocess, os, sys, time, tempfile,string +import subprocess, os, sys, time, tempfile,string,plinkbinJZ galhtmlprefix = """<?xml version="1.0" encoding="utf-8" ?> <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> @@ -279,3 +279,64 @@ rsdict = dict(zip(rslist,rslist)) mfile.close() return markers,snpcols,rslist,rsdict + +def openOrMakeLDreduced(basename,newfpath,plinke): + """ move out of the way - highly specific plink function to create or open + an ld reduced and thinned data set for one of the ibs/grr methods.. + this should be part of the plinkJZ stuff - or bought in here maybe + """ + ldr = '%s_INDEP_THIN' % basename # we store ld reduced and thinned data + ldreduced = os.path.join(newfpath,ldr) + ped = None + loglines = [] + vclbase = [] + ldbedname = '%s.bed' % ldreduced + ldpedname = '%s.ped' % ldreduced + bedname = '%s.bed' % basename + pedname = '%s.ped' % basename + ldbedfn = os.path.join(newfpath,ldbedname) + ldpedfn = os.path.join(newfpath,ldpedname) + bedfn = os.path.join(newfpath,bedname) + pedfn = os.path.join(newfpath,pedname) + bmap = os.path.join(newfpath,'%s.bim' % basename) + pmap = os.path.join(newfpath,'%s.map' % basename) + if os.path.exists(ldbedfn): # joy. already done + ped = plinkbinJZ.BPed(ldreduced) + ped.parse(quick=True) + return ped,loglines + if os.path.exists(ldpedfn): # why bother - for completeness I guess + ped = plinkbinJZ.LPed(ldreduced) + ped.parse() + return ped,loglines + if os.path.exists(bedfn): # run ld prune and thin and save these for next time + nsnp = len(open(bmap,'r').readlines()) + plinktasks = [['--bfile',basename,'--indep-pairwise 50 40 0.2','--out %s' % basename], + ['--bfile',basename,'--extract %s.prune.in --make-bed --out %s_INDEP' % (basename, basename)]] + if nsnp < 100: # if 9 snps --thin 0.1 will happily return 0 snps + plinktasks += [['--bfile %s_INDEP --make-bed --out %s' % (basename,ldreduced)],] + else: # thin rather than copy + plinktasks += [['--bfile',basename,'--extract %s.prune.in --make-bed --out %s' % (basename, ldreduced)]] + # subset of ld independent markers for eigenstrat and other requirements + vclbase = [plinke,'--noweb'] + loglines = pruneLD(plinktasks=plinktasks,cd=newfpath,vclbase = vclbase) + ped = plinkbinJZ.BPed(ldreduced) + return ped,loglines + if pedname and os.path.exists(pedfn): # screw it - return a bed - quicker to process + nsnp = len(open(pmap,'r').readlines()) + if nsnp > 100: + plinktasks = [['--file',basename,'--make-bed','--out',basename], + ['--bfile',basename,'--indep-pairwise 50 40 0.2','--out %s' % basename], + ['--bfile',basename,'--extract %s.prune.in --make-bed --out %s_INDEP' % (basename, basename)], + ['--bfile %s_INDEP --thin 0.1 --recode --out %s' % (bedname,ldreduced),]] + else: # no thin step + plinktasks = [['--file',basename,'--make-bed','--out',basename], + ['--bfile',basename,'--indep-pairwise 50 40 0.2','--out %s' % basename], + ['--bfile',basename,'--extract %s.prune.in --make-bed --out %s' % (basename, ldreduced)]] + + # subset of ld independent markers for eigenstrat and other requirements + vclbase = [plinke,'--noweb'] + loglines = pruneLD(plinktasks=plinktasks,cd=newfpath,vclbase = vclbase) + ped = plinkbinJZ.BPed(os.path.splitext(ldbedfn)[0]) + ped.parse(quick=True) + return ped,loglines +

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