January 2009 - galaxy-dev - lists.galaxyproject.org

[hg] galaxy 1727: Add fetch_eggs option to pull for other platfo...
by Nate Coraor 30 Jan '09

30 Jan '09

details: http://www.bx.psu.edu/hg/galaxy/rev/e1e119b0bd17 changeset: 1727:e1e119b0bd17 user: Nate Coraor <nate(a)bx.psu.edu> date: Fri Jan 30 11:37:18 2009 -0500 description: Add fetch_eggs option to pull for other platforms (e.g. cluster nodes) 2 file(s) affected in this change: scripts/fetch_eggs.py scripts/get_platforms.py diffs (47 lines): diff -r 9a06f9910524 -r e1e119b0bd17 scripts/fetch_eggs.py --- a/scripts/fetch_eggs.py Tue Jan 27 17:12:04 2009 -0500 +++ b/scripts/fetch_eggs.py Fri Jan 30 11:37:18 2009 -0500 @@ -1,9 +1,13 @@ """ -usage: fetch_eggs.py [egg_name] +usage: fetch_eggs.py [egg_name] [platform] With no arguments, fetches all eggs necessary according to the settings in universe_wsgi.ini. egg_name - Fetch only this egg (as defined in eggs.ini) or 'all' for all eggs (even those not required by your settings). + platform - Fetch eggs for a specific platform (if not provided, fetch + eggs for *this* platform). Useful for fetching eggs for cluster + nodes which are of a different architecture than the head node. + Platform name can be determined with the get_platforms.py script. """ import os, sys, logging @@ -17,6 +21,8 @@ from galaxy.eggs import * c = Crate() +if len( sys.argv ) == 3: + c.platform = { 'peak' : sys.argv[2].rsplit('-',1)[0], 'galaxy' : sys.argv[2] } c.parse() try: if len( sys.argv ) == 1: diff -r 9a06f9910524 -r e1e119b0bd17 scripts/get_platforms.py --- a/scripts/get_platforms.py Tue Jan 27 17:12:04 2009 -0500 +++ b/scripts/get_platforms.py Fri Jan 30 11:37:18 2009 -0500 @@ -1,9 +1,12 @@ #!/usr/bin/env python -import sys +import os, sys assert sys.version_info[:2] >= ( 2, 4 ) -from eggs import get_full_platform, get_noplatform -print get_noplatform() -print get_full_platform() +lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ), "..", "lib" ) ) +sys.path.append( lib ) + +from galaxy.eggs import get_platform +print get_platform() +print get_platform( True )

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[hg] galaxy 1728: Fix annotation profiler interpreter to be pyth...
by Nate Coraor 30 Jan '09

30 Jan '09

details: http://www.bx.psu.edu/hg/galaxy/rev/cabfdc9dea12 changeset: 1728:cabfdc9dea12 user: Nate Coraor <nate(a)bx.psu.edu> date: Fri Jan 30 11:37:51 2009 -0500 description: Fix annotation profiler interpreter to be python, not python2.4 1 file(s) affected in this change: tools/annotation_profiler/annotation_profiler.xml diffs (11 lines): diff -r e1e119b0bd17 -r cabfdc9dea12 tools/annotation_profiler/annotation_profiler.xml --- a/tools/annotation_profiler/annotation_profiler.xml Fri Jan 30 11:37:18 2009 -0500 +++ b/tools/annotation_profiler/annotation_profiler.xml Fri Jan 30 11:37:51 2009 -0500 @@ -1,6 +1,6 @@ <tool id="Annotation_Profiler_0" name="Profile Annotations" Version="1.0.0"> <description>for a set of genomic intervals</description> - <command interpreter="python2.4">annotation_profiler_for_interval.py -i $input1 -c ${input1.metadata.chromCol} -s ${input1.metadata.startCol} -e ${input1.metadata.endCol} -o $out_file1 $keep_empty -p /depot/data2/galaxy/annotation_profiler/$dbkey $summary -l ${GALAXY_DATA_INDEX_DIR}/shared/ucsc/chrom/${dbkey}.len -b 3 -t $table_names</command> + <command interpreter="python">annotation_profiler_for_interval.py -i $input1 -c ${input1.metadata.chromCol} -s ${input1.metadata.startCol} -e ${input1.metadata.endCol} -o $out_file1 $keep_empty -p /depot/data2/galaxy/annotation_profiler/$dbkey $summary -l ${GALAXY_DATA_INDEX_DIR}/shared/ucsc/chrom/${dbkey}.len -b 3 -t $table_names</command> <inputs> <param format="interval" name="input1" type="data" label="Choose Intervals"> <validator type="dataset_metadata_in_file" filename="annotation_profiler_valid_builds.txt" metadata_name="dbkey" metadata_column="0" message="Profiling is not currently available for this species."/>

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[hg] galaxy 1726: More fixes to eggs.require()
by Nate Coraor 27 Jan '09

27 Jan '09

details: http://www.bx.psu.edu/hg/galaxy/rev/9a06f9910524 changeset: 1726:9a06f9910524 user: Nate Coraor <nate(a)bx.psu.edu> date: Tue Jan 27 17:12:04 2009 -0500 description: More fixes to eggs.require() 1 file(s) affected in this change: lib/galaxy/eggs/__init__.py diffs (35 lines): diff -r 7411b119a3c9 -r 9a06f9910524 lib/galaxy/eggs/__init__.py --- a/lib/galaxy/eggs/__init__.py Tue Jan 27 16:17:22 2009 -0500 +++ b/lib/galaxy/eggs/__init__.py Tue Jan 27 17:12:04 2009 -0500 @@ -527,7 +527,6 @@ pkg_resources.working_set.require( pkg ) else: pkg_resources.working_set.require( "%s==%s" % ( name, egg.get_vertag() ) ) - return except pkg_resources.VersionConflict, e: # there's a conflicting egg on the pythonpath, remove it dist = e.args[0] @@ -539,10 +538,13 @@ working_set.entries.remove( entry ) break else: - raise # some path weirdness has prevented us from finding the offender + location = None del working_set.by_key[dist.key] working_set.entry_keys[entry] = [] sys.path.remove(entry) + require( pkg ) + if location is not None and not location.endswith( '.egg' ): + working_set.entries.append( location ) # re-add to the set if it's a dir. except pkg_resources.DistributionNotFound, e: # the initial require itself is the first dep, but it can have # multiple deps, which will be fetched by the require below. @@ -555,7 +557,7 @@ if not egg.have: if not egg.fetch(): raise EggNotFetchable( egg.name ) - require( pkg ) + require( pkg ) # convenience stuff def get_ucs():

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[hg] galaxy 1725: Adding modified hyphy functional test output f...
by gua110＠scofield.bx.psu.edu 27 Jan '09

27 Jan '09

details: http://www.bx.psu.edu/hg/galaxy/rev/7411b119a3c9 changeset: 1725:7411b119a3c9 user: guru date: Tue Jan 27 16:17:22 2009 -0500 description: Adding modified hyphy functional test output files, which have changed as the new version of HYPHY is installed on Galaxy. Also changing version numbers for all the affected tools. 8 file(s) affected in this change: test-data/branchlength_out.dat test-data/dnds_out.tabular test-data/nj_tree_newick_out.dat tools/hyphy/hyphy_branch_lengths_wrapper.xml tools/hyphy/hyphy_dnds_wrapper.xml tools/hyphy/hyphy_nj_tree_wrapper.xml tools/regVariation/microsats_mutability.xml tools/stats/grouping.xml diffs (140 lines): diff -r 546e2d835e16 -r 7411b119a3c9 test-data/branchlength_out.dat --- a/test-data/branchlength_out.dat Tue Jan 27 14:48:51 2009 -0500 +++ b/test-data/branchlength_out.dat Tue Jan 27 16:17:22 2009 -0500 @@ -9,25 +9,25 @@ 1 Total Tree 3.45679e-30 2.60643e-34 2.54701e-20 2 hg17.chr7(+):26907310-26907326|hg17_1 1.48148e-31 0 0.0915385 2 panTro1.chr6(+):28037328-28037344|panTro1_1 1.48148e-31 0 0.0915385 -2 Node1 1.48148e-31 0 0.0915385 -2 mm5.chr6(+):52104031-52104047|mm5_1 1.48148e-31 0 0.0915385 -2 rn3.chr4(+):80734404-80734420|rn3_1 0.0435496 0.00241411 0.219651 +2 Node1 6.69055e-19 0 0.0915385 +2 mm5.chr6(+):52104031-52104047|mm5_1 5.00368e-19 0 0.0915385 +2 rn3.chr4(+):80734404-80734420|rn3_1 0.0435526 0.00241411 0.219651 2 Node4 1.48148e-31 0 0.0915385 -2 canFam1.chr14(+):42826418-42826434|canFam1_1 1.48148e-31 0 0.0915385 -2 Total Tree 0.0435496 0.00241411 0.219655 +2 canFam1.chr14(+):42826418-42826434|canFam1_1 1.76058e-19 0 0.0915385 +2 Total Tree 0.0435526 0.00241411 0.219651 3 hg17.chr7(+):26907326-26907338|hg17_2 1.70011e-31 0 0.143452 3 panTro1.chr6(+):28037344-28037356|panTro1_2 1.70011e-31 0 0.143452 -3 Node1 1.70011e-31 0 0.143452 +3 Node1 1.27931e-17 0 0.143452 3 mm5.chr6(+):52104047-52104059|mm5_2 1.70011e-31 0 0.143452 3 rn3.chr4(+):80734420-80734432|rn3_2 0 0 0.143452 -3 Node4 1.70011e-31 0 0.143452 +3 Node4 0 0 0.143452 3 canFam1.chr14(+):42826434-42826446|canFam1_2 1.70011e-31 0 0.143452 -3 Total Tree 1.02006e-30 7.69131e-35 7.51597e-21 -4 hg17.chr7(+):26907338-26907654|hg17_3 1.98983e-31 0 0.0066257 -4 panTro1.chr6(+):28037356-28037672|panTro1_3 1.98983e-31 0 0.0066257 -4 Node1 0.0148072 0.00246575 0.0381554 -4 mm5.chr6(+):52104059-52104375|mm5_3 0.0275943 0.0109457 0.0548099 -4 rn3.chr4(+):80734432-80734748|rn3_3 0.0217662 0.00736615 0.0466518 -4 Node4 0.045162 0.0224707 0.0792981 -4 canFam1.chr14(+):42826446-42826762|canFam1_3 0.0320463 0.0139406 0.0605161 -4 Total Tree 0.141376 0.100446 0.192464 +3 Total Tree 1.27931e-17 9.64599e-22 9.4261e-08 +4 hg17.chr7(+):26907338-26907654|hg17_3 1.98974e-31 0 0.00662576 +4 panTro1.chr6(+):28037356-28037672|panTro1_3 1.98974e-31 0 0.00662576 +4 Node1 0.014806 0.00246541 0.0381554 +4 mm5.chr6(+):52104059-52104375|mm5_3 0.0275935 0.0109456 0.0548103 +4 rn3.chr4(+):80734432-80734748|rn3_3 0.0217688 0.00736645 0.0466551 +4 Node4 0.0451597 0.0224663 0.0792997 +4 canFam1.chr14(+):42826446-42826762|canFam1_3 0.0320496 0.013941 0.0605175 +4 Total Tree 0.141378 0.100447 0.192467 diff -r 546e2d835e16 -r 7411b119a3c9 test-data/dnds_out.tabular --- a/test-data/dnds_out.tabular Tue Jan 27 14:48:51 2009 -0500 +++ b/test-data/dnds_out.tabular Tue Jan 27 16:17:22 2009 -0500 @@ -1,12 +1,12 @@ BLOCK BP S_sites NS_sites Stop_codons LogL omega omega_range AC AT CG CT GT Tree -1 1554 355.669 1129.12 1 -2747.41 0.101159 0.0765061-0.130636 1 1 1 1 1 (human:0,chimp:0.00240762,mouse:0.146649) -2 3795 924.935 2749.35 1 -5781.01 0.0179485 0.0119925-0.02562 1 1 1 1 1 (human:0.0004305,chimp:0.00147714,mouse:0.144943) -3 1194 272.323 881.914 1 -2043.72 0.0578339 0.0372207-0.0849736 1 1 1 1 1 (human:0.00285309,chimp:0.00410455,mouse:0.11988) -4 1146 248.261 850.364 1 -1871.67 0.012771 0.00548036-0.0247371 1 1 1 1 1 (human:0,chimp:0.00093192,mouse:0.147209) -5 1500 366.374 1086.09 2 -2522.97 0.0331894 0.0203743-0.0505255 1 1 1 1 1 (human:0,chimp:0.00225976,mouse:0.156089) -6 3444 824.107 2475.54 1 -5459.18 0.0439755 0.0326426-0.0576899 1 1 1 1 1 (human:0.000512784,chimp:0.00203485,mouse:0.126653) -7 2175 505.186 1587.7 0 -3307.52 0.0712367 0.0564019-0.088443 1 1 1 1 1 (human:0.00229486,chimp:0.00236745,mouse:0.226418) -8 3519 792.702 2601.36 0 -6219.39 0.0669992 0.0568977-0.078214 1 1 1 1 1 (human:0.00103092,chimp:0.00431199,mouse:0.251293) -9 501 100.22 376.039 1 -834.329 0.13041 0.0835498-0.192248 1 1 1 1 1 (human:0,chimp:0,mouse:0.150462) -10 633 160.252 453.228 1 -618.997 0.0150887 0.00250412-0.0467112 1 1 1 1 1 (human:0,chimp:0.00611143,mouse:0.104315) -11 915 229.705 658.82 0 -1664.02 0.299737 0.227826-0.385548 1 1 1 1 1 (human:0.0045721,chimp:0,mouse:0.145563) +1 1554 355.669 1129.12 1 -2747.41 0.101087 0.0764772-0.130598 1 1 1 1 1 (human:0,chimp:0.0024086,mouse:0.146678) +2 3795 924.935 2749.35 1 -5781.01 0.0179487 0.0119926-0.0256204 1 1 1 1 1 (human:0.000420365,chimp:0.00148429,mouse:0.144946) +3 1194 272.323 881.914 1 -2043.72 0.057806 0.0372158-0.0849625 1 1 1 1 1 (human:0.00284622,chimp:0.0041096,mouse:0.119889) +4 1146 248.261 850.364 1 -1871.67 0.0127683 0.00548023-0.0247365 1 1 1 1 1 (human:1.64845e-31,chimp:0.000931909,mouse:0.147211) +5 1500 366.374 1086.09 2 -2522.97 0.0331759 0.0203729-0.0505178 1 1 1 1 1 (human:0,chimp:0.00225973,mouse:0.156094) +6 3444 824.107 2475.54 1 -5459.18 0.0439729 0.032642-0.0576888 1 1 1 1 1 (human:0.000513623,chimp:0.00203456,mouse:0.126654) +7 2175 505.186 1587.7 0 -3307.52 0.0711481 0.0563562-0.0883841 1 1 1 1 1 (human:0.0022939,chimp:0.00236854,mouse:0.226516) +8 3519 792.702 2601.36 0 -6219.39 0.0669805 0.0568888-0.0782017 1 1 1 1 1 (human:0.00102641,chimp:0.00431646,mouse:0.25132) +9 501 100.22 376.039 1 -834.329 0.130019 0.0833975-0.191896 1 1 1 1 1 (human:0,chimp:2.19778e-31,mouse:0.150592) +10 633 160.252 453.228 1 -618.997 0.0150806 0.00250396-0.0467057 1 1 1 1 1 (human:0,chimp:0.00611203,mouse:0.104319) +11 915 229.705 658.82 0 -1664.02 0.299406 0.227634-0.385273 1 1 1 1 1 (human:0.00457505,chimp:3.44909e-31,mouse:0.145589) diff -r 546e2d835e16 -r 7411b119a3c9 test-data/nj_tree_newick_out.dat --- a/test-data/nj_tree_newick_out.dat Tue Jan 27 14:48:51 2009 -0500 +++ b/test-data/nj_tree_newick_out.dat Tue Jan 27 16:17:22 2009 -0500 @@ -1,10 +1,10 @@ -0 ((hg17,panTro1),rheMac2,(rn3,mm7)) ((hg17.chr7(+):127471195-127471526|hg17_0:0.00346971,panTro1.chr6(+):129885076-129885407|panTro1_0:0.00260712):0.0126114,rheMac2.chr3(+):165787989-165788319|rheMac2_0:0.028188,(rn3.chr4(+):56178191-56178473|rn3_0:0.0617996,mm7.chr6(+):28984529-28984886|mm7_0:0.0662353):0.305784) +0 (hg17,panTro1,(rheMac2,(rn3,mm7))) (hg17.chr7(+):127471195-127471526|hg17_0:0.00283776,panTro1.chr6(+):129885076-129885407|panTro1_0:0.00323907,(rheMac2.chr3(+):165787989-165788319|rheMac2_0:0.0324438,(rn3.chr4(+):56178191-56178473|rn3_0:0.0264183,mm7.chr6(+):28984529-28984886|mm7_0:0.148227):0.457076):0.00849339) 1 ((hg17,panTro1),mm7,rheMac2) ((hg17.chr7(+):127471526-127471584|hg17_1:0.00446699,panTro1.chr6(+):129885407-129885465|panTro1_1:0.013401):0.00483543,mm7.chr6(+):28984886-28984940|mm7_1:999.986,rheMac2.chr3(+):165788319-165788377|rheMac2_1:0.0137694) -2 (((hg17,panTro1),rheMac2),(canFam2,dasNov1),(bosTau2,rn3)) (((hg17.chr7(+):127471584-127471688|hg17_2:0.00234609,panTro1.chr6(+):129885465-129885569|panTro1_2:0.0173725):0.0101799,rheMac2.chr3(+):165788377-165788482|rheMac2_2:0.063065):0.106752,(canFam2.chr14(-):11090703-11090811|canFam2_2:0.187046,dasNov1.scaffold_256527(+):298-392|dasNov1_2:0.0930379):0.0263477,(bosTau2.chr4(-):50243931-50244034|bosTau2_2:0.154553,rn3.chr4(+):56182200-56182295|rn3_2:0.21476):0.0231563) -3 ((hg17,panTro1),rheMac2,(rn3,((bosTau2,dasNov1),canFam2))) ((hg17.chr7(+):127471688-127471871|hg17_3:0.0186952,panTro1.chr6(+):129885569-129885752|panTro1_3:0.00389261):0.024721,rheMac2.chr3(+):165788482-165788684|rheMac2_3:0.0326957,(rn3.chr4(+):56182295-56182489|rn3_3:0.151674,((bosTau2.chr4(-):50243792-50243930|bosTau2_3:0.0510929,dasNov1.scaffold_256527(+):393-625|dasNov1_3:0.119004):0.0284421,canFam2.chr14(-):11090345-11090505|canFam2_3:0.0489193):0.0426697):0.0457765) -4 ((hg17,rheMac2),panTro1,((bosTau2,canFam2),dasNov1)) ((hg17.chr7(+):127471871-127471910|hg17_4:0,rheMac2.chr3(+):165788684-165788723|rheMac2_4:0.0586327):0.0163653,panTro1.chr6(+):129885752-129885791|panTro1_4:0,((bosTau2.chr4(-):50243734-50243773|bosTau2_4:0.462227,canFam2.chr14(-):11090081-11090120|canFam2_4:0.199596):0.112898,dasNov1.scaffold_256527(+):625-665|dasNov1_4:0.160286):0.163376) -5 (((hg17,panTro1),rheMac2),((mm7,rn3),dasNov1),(bosTau2,canFam2)) (((hg17.chr7(+):127471910-127472074|hg17_5:0,panTro1.chr6(+):129885791-129885955|panTro1_5:0.0185501):0.0510514,rheMac2.chr3(+):165788723-165788885|rheMac2_5:0.0284199):0.105274,((mm7.chr6(+):28990714-28990875|mm7_5:0.110927,rn3.chr4(+):56183448-56183705|rn3_5:0):0.18866,dasNov1.scaffold_256527(+):665-786|dasNov1_5:0.1964):0.0403849,(bosTau2.chr4(-):50243566-50243734|bosTau2_5:0.169804,canFam2.chr14(-):11089913-11090081|canFam2_5:0.135334):0.0416476) -6 (hg17,panTro1,(rheMac2,((mm7,rn3),(canFam2,dasNov1)))) (hg17.chr7(+):127472074-127472258|hg17_6:0.00678011,panTro1.chr6(+):129885955-129886139|panTro1_6:0,(rheMac2.chr3(+):165788885-165789069|rheMac2_6:0.0438345,((mm7.chr6(+):28990875-28991025|mm7_6:0.0290692,rn3.chr4(+):56183705-56183879|rn3_6:0.13263):0.168495,(canFam2.chr14(-):11089743-11089913|canFam2_6:0.138698,dasNov1.scaffold_256527(+):786-964|dasNov1_6:0.1994):0.0351372):0.128281):0.0237393) -7 (((hg17,(canFam2,dasNov1)),panTro1),rheMac2,(mm7,rn3)) (((hg17.chr7(+):127472258-127472280|hg17_7:0,(canFam2.chr14(-):11089526-11089548|canFam2_7:0.513656,dasNov1.scaffold_256527(+):964-987|dasNov1_7:0.205512):0.34336):0,panTro1.chr6(+):129886139-129886161|panTro1_7:0):0,rheMac2.chr3(+):165789069-165789091|rheMac2_7:0,(mm7.chr6(+):28991025-28991048|mm7_7:0.0744383,rn3.chr4(+):56183879-56183902|rn3_7:0.0195258):125.2) -8 (((hg17,panTro1),rheMac2),(rn3,canFam2),dasNov1) (((hg17.chr7(+):127472280-127472681|hg17_8:0.00751116,panTro1.chr6(+):129886161-129886562|panTro1_8:2.84007e-05):0.0348269,rheMac2.chr3(+):165789091-165789492|rheMac2_8:0.0280716):0.115196,(rn3.chr4(+):56183902-56184219|rn3_8:0.16879,canFam2.chr14(-):11089143-11089523|canFam2_8:0.158484):0.0249651,dasNov1.scaffold_256527(+):987-1401|dasNov1_8:0.21816) -9 (((hg17,panTro1),canFam2),rheMac2,dasNov1) (((hg17.chr7(+):127472681-127472715|hg17_9:0.0115551,panTro1.chr6(+):129886562-129886596|panTro1_9:0.0221032):0.044958,canFam2.chr14(-):11089108-11089143|canFam2_9:0.218642):0.030703,rheMac2.chr3(+):165789492-165789526|rheMac2_9:0.00773783,dasNov1.scaffold_256527(+):1401-1433|dasNov1_9:0.113241) +2 ((((hg17,panTro1),rheMac2),(canFam2,dasNov1)),bosTau2,rn3) ((((hg17.chr7(+):127471584-127471688|hg17_2:0.00103752,panTro1.chr6(+):129885465-129885569|panTro1_2:0.018681):0.00493709,rheMac2.chr3(+):165788377-165788482|rheMac2_2:0.0691856):0.106183,(canFam2.chr14(-):11090703-11090811|canFam2_2:0.213381,dasNov1.scaffold_256527(+):298-392|dasNov1_2:0.123834):0.0305914):0.028679,bosTau2.chr4(-):50243931-50244034|bosTau2_2:0.170682,rn3.chr4(+):56182200-56182295|rn3_2:0.285956) +3 ((hg17,panTro1),rheMac2,(rn3,(bosTau2,(canFam2,dasNov1)))) ((hg17.chr7(+):127471688-127471871|hg17_3:0.0225878,panTro1.chr6(+):129885569-129885752|panTro1_3:0):0.0221216,rheMac2.chr3(+):165788482-165788684|rheMac2_3:0.0429855,(rn3.chr4(+):56182295-56182489|rn3_3:0.286513,(bosTau2.chr4(-):50243792-50243930|bosTau2_3:0.135108,(canFam2.chr14(-):11090345-11090505|canFam2_3:0.0418005,dasNov1.scaffold_256527(+):393-625|dasNov1_3:0.198071):0.0128256):0.0852898):0.0472209) +4 ((hg17,rheMac2),panTro1,((bosTau2,canFam2),dasNov1)) ((hg17.chr7(+):127471871-127471910|hg17_4:0,rheMac2.chr3(+):165788684-165788723|rheMac2_4:0.0586327):0.0166268,panTro1.chr6(+):129885752-129885791|panTro1_4:0,((bosTau2.chr4(-):50243734-50243773|bosTau2_4:0.462377,canFam2.chr14(-):11090081-11090120|canFam2_4:0.199446):0.119837,dasNov1.scaffold_256527(+):625-665|dasNov1_4:0.17977):0.172715) +5 (((hg17,panTro1),rheMac2),(mm7,rn3),((bosTau2,dasNov1),canFam2)) (((hg17.chr7(+):127471910-127472074|hg17_5:0.000139728,panTro1.chr6(+):129885791-129885955|panTro1_5:0.0184104):0.05206,rheMac2.chr3(+):165788723-165788885|rheMac2_5:0.0285966):0.0250925,(mm7.chr6(+):28990714-28990875|mm7_5:0.123289,rn3.chr4(+):56183448-56183705|rn3_5:0.0718529):0.38361,((bosTau2.chr4(-):50243566-50243734|bosTau2_5:0.181878,dasNov1.scaffold_256527(+):665-786|dasNov1_5:0.429124):0.0618692,canFam2.chr14(-):11089913-11090081|canFam2_5:0.133548):0.11305) +6 ((hg17,panTro1),rheMac2,((mm7,rn3),(canFam2,dasNov1))) ((hg17.chr7(+):127472074-127472258|hg17_6:0.00549431,panTro1.chr6(+):129885955-129886139|panTro1_6:0):0.0241181,rheMac2.chr3(+):165788885-165789069|rheMac2_6:0.0447415,((mm7.chr6(+):28990875-28991025|mm7_6:0.0851965,rn3.chr4(+):56183705-56183879|rn3_6:0.109546):0.319094,(canFam2.chr14(-):11089743-11089913|canFam2_6:0.186816,dasNov1.scaffold_256527(+):786-964|dasNov1_6:0.219003):0.0699235):0.0966238) +7 (((hg17,(canFam2,dasNov1)),panTro1),rheMac2,(mm7,rn3)) (((hg17.chr7(+):127472258-127472280|hg17_7:0,(canFam2.chr14(-):11089526-11089548|canFam2_7:0.572157,dasNov1.scaffold_256527(+):964-987|dasNov1_7:0.212507):0.327632):0,panTro1.chr6(+):129886139-129886161|panTro1_7:0):0,rheMac2.chr3(+):165789069-165789091|rheMac2_7:0,(mm7.chr6(+):28991025-28991048|mm7_7:0.0708909,rn3.chr4(+):56183879-56183902|rn3_7:0.0230732):125.221) +8 (((hg17,panTro1),rheMac2),(rn3,canFam2),dasNov1) (((hg17.chr7(+):127472280-127472681|hg17_8:0.00753956,panTro1.chr6(+):129886161-129886562|panTro1_8:0):0.0353922,rheMac2.chr3(+):165789091-165789492|rheMac2_8:0.0278572):0.0967916,(rn3.chr4(+):56183902-56184219|rn3_8:0.379264,canFam2.chr14(-):11089143-11089523|canFam2_8:0.207268):0.0346594,dasNov1.scaffold_256527(+):987-1401|dasNov1_8:0.268281) +9 (hg17,((rheMac2,dasNov1),canFam2),panTro1) (hg17.chr7(+):127472681-127472715|hg17_9:0.0183718,((rheMac2.chr3(+):165789492-165789526|rheMac2_9:0,dasNov1.scaffold_256527(+):1401-1433|dasNov1_9:0.160078):0.0595979,canFam2.chr14(-):11089108-11089143|canFam2_9:0.237132):0.0383088,panTro1.chr6(+):129886562-129886596|panTro1_9:0.0152865) diff -r 546e2d835e16 -r 7411b119a3c9 tools/hyphy/hyphy_branch_lengths_wrapper.xml --- a/tools/hyphy/hyphy_branch_lengths_wrapper.xml Tue Jan 27 14:48:51 2009 -0500 +++ b/tools/hyphy/hyphy_branch_lengths_wrapper.xml Tue Jan 27 16:17:22 2009 -0500 @@ -1,4 +1,4 @@ -<?xml version="1.0"?> +<?xml version="1.1.0"?> <tool name="Branch Lengths" id="hyphy_branch_lengths_wrapper1"> <description>Estimation</description> diff -r 546e2d835e16 -r 7411b119a3c9 tools/hyphy/hyphy_dnds_wrapper.xml --- a/tools/hyphy/hyphy_dnds_wrapper.xml Tue Jan 27 14:48:51 2009 -0500 +++ b/tools/hyphy/hyphy_dnds_wrapper.xml Tue Jan 27 16:17:22 2009 -0500 @@ -1,4 +1,4 @@ -<?xml version="1.0"?> +<?xml version="1.1.0"?> <tool name="dN/dS Ratio" id="hyphy_dnds_wrapper1"> <description>Estimation</description> diff -r 546e2d835e16 -r 7411b119a3c9 tools/hyphy/hyphy_nj_tree_wrapper.xml --- a/tools/hyphy/hyphy_nj_tree_wrapper.xml Tue Jan 27 14:48:51 2009 -0500 +++ b/tools/hyphy/hyphy_nj_tree_wrapper.xml Tue Jan 27 16:17:22 2009 -0500 @@ -1,4 +1,4 @@ -<?xml version="1.0"?> +<?xml version="1.1.0"?> <tool name="Neighbor Joining Tree" id="hyphy_nj_tree_wrapper1"> <description>Builder</description> diff -r 546e2d835e16 -r 7411b119a3c9 tools/regVariation/microsats_mutability.xml --- a/tools/regVariation/microsats_mutability.xml Tue Jan 27 14:48:51 2009 -0500 +++ b/tools/regVariation/microsats_mutability.xml Tue Jan 27 16:17:22 2009 -0500 @@ -1,4 +1,4 @@ -<tool id="microsats_mutability1" name="Estimate microsatellite mutability" version="1.0.0"> +<tool id="microsats_mutability1" name="Estimate microsatellite mutability" version="1.1.0"> <description>by specified attributes</description> <command interpreter="python"> microsats_mutability.py diff -r 546e2d835e16 -r 7411b119a3c9 tools/stats/grouping.xml --- a/tools/stats/grouping.xml Tue Jan 27 14:48:51 2009 -0500 +++ b/tools/stats/grouping.xml Tue Jan 27 16:17:22 2009 -0500 @@ -1,4 +1,4 @@ -<tool id="Grouping1" name="Group" version="1.4.0"> +<tool id="Grouping1" name="Group" version="1.5.0"> <description>data by a column and perform aggregate operation on other columns.</description> <command interpreter="python"> grouping.py

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[hg] galaxy 1724: upgrade bx-python to rev 460
by Nate Coraor 27 Jan '09

27 Jan '09

details: http://www.bx.psu.edu/hg/galaxy/rev/546e2d835e16 changeset: 1724:546e2d835e16 user: Nate Coraor <nate(a)bx.psu.edu> date: Tue Jan 27 14:48:51 2009 -0500 description: upgrade bx-python to rev 460 1 file(s) affected in this change: eggs.ini diffs (18 lines): diff -r 6e88248dcc84 -r 546e2d835e16 eggs.ini --- a/eggs.ini Mon Jan 26 14:48:45 2009 -0500 +++ b/eggs.ini Tue Jan 27 14:48:51 2009 -0500 @@ -55,12 +55,12 @@ MySQL_python = _5.0.67_static python_lzo = _static flup = .dev_r2311 -bx_python = _dev_r459 +bx_python = _dev_r460 nose = .dev_r101 ; source location, necessary for scrambling [source] -bx_python = http://dist.g2.bx.psu.edu/bx-python_dist-r459.tar.bz2 +bx_python = http://dist.g2.bx.psu.edu/bx-python_dist-r460.tar.bz2 Cheetah = http://voxel.dl.sourceforge.net/sourceforge/cheetahtemplate/Cheetah-1.0.tar… DRMAA_python = http://gridengine.sunsource.net/files/documents/7/36/DRMAA-python-0.2.tar.gz MySQL_python = http://superb-west.dl.sourceforge.net/sourceforge/mysql-python/MySQL-python… http://mysql.mirrors.pair.com/Downloads/MySQL-5.0/mysql-5.0.67.tar.gz

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[hg] galaxy 1723: Fix For MAF Filter tool.
by Greg Von Kuster 26 Jan '09

26 Jan '09

details: http://www.bx.psu.edu/hg/galaxy/rev/6e88248dcc84 changeset: 1723:6e88248dcc84 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Mon Jan 26 14:48:45 2009 -0500 description: Fix For MAF Filter tool. Looks like when grouping parameter types were updated to be recursively wrapped properly, this tool was not updated. 1 file(s) affected in this change: tools/maf/maf_filter.xml diffs (32 lines): diff -r 2a81c4b95e20 -r 6e88248dcc84 tools/maf/maf_filter.xml --- a/tools/maf/maf_filter.xml Mon Jan 26 14:41:00 2009 -0500 +++ b/tools/maf/maf_filter.xml Mon Jan 26 14:48:45 2009 -0500 @@ -104,22 +104,22 @@ #if $len( $maf_filter['species1_attributes']['filter_condition'] ) == 0: #continue #end if - primary_component = maf_block.get_component_by_src_start( """$maf_filter['species1'].encode( 'string_escape' )""".decode( 'string_escape' ) ) + primary_component = maf_block.get_component_by_src_start( """$maf_filter['species1'].value.encode( 'string_escape' )""".decode( 'string_escape' ) ) if primary_component is not None: #if $maf_filter['species1_attributes']['species1_attribute_type'] == 'attribute_chr': - if primary_component.src.split( "." )[-1] $is_isnot_valid.get( $maf_filter['species1_attributes']['species1_is_isnot'].strip(), 'is in' ) """$maf_filter['species1_attributes']['species1_attribute'].encode( 'string_escape' )""".decode( 'string_escape' ).split( "," ): + if primary_component.src.split( "." )[-1] $is_isnot_valid.get( $maf_filter['species1_attributes']['species1_is_isnot'].value.strip(), 'is in' ) """$maf_filter['species1_attributes']['species1_attribute'].value.encode( 'string_escape' )""".decode( 'string_escape' ).split( "," ): #else - if primary_component.strand $is_isnot_valid.get( $maf_filter['species1_attributes']['species1_is_isnot'].strip(), '==' ) """$maf_filter['species1_attributes']['species1_attribute'].encode( 'string_escape' )""".decode( 'string_escape' ): + if primary_component.strand $is_isnot_valid.get( $maf_filter['species1_attributes']['species1_is_isnot'].value.strip(), '==' ) """$maf_filter['species1_attributes']['species1_attribute'].value.encode( 'string_escape' )""".decode( 'string_escape' ): #end if #for $filter_condition in $maf_filter['species1_attributes']['filter_condition']: - secondary_component = maf_block.get_component_by_src_start( """$filter_condition['species2'].encode( 'string_escape' )""".decode( 'string_escape' ) ) + secondary_component = maf_block.get_component_by_src_start( """$filter_condition['species2'].value.encode( 'string_escape' )""".decode( 'string_escape' ) ) #if $filter_condition['species2_attributes']['species2_attribute_type'] == 'attribute_chr': if secondary_component is not None: - if not ( secondary_component.src.split( "." )[-1] $is_isnot_valid.get( $filter_condition['species2_attributes']['species2_is_isnot'].strip(), 'is in' ) """$filter_condition['species2_attributes']['species2_attribute'].encode( 'string_escape' )""".decode( 'string_escape' ).split( "," ) ): + if not ( secondary_component.src.split( "." )[-1] $is_isnot_valid.get( $filter_condition['species2_attributes']['species2_is_isnot'].value.strip(), 'is in' ) """$filter_condition['species2_attributes']['species2_attribute'].value.encode( 'string_escape' )""".decode( 'string_escape' ).split( "," ) ): return False #else: if secondary_component is not None: - if not ( secondary_component.strand $is_isnot_valid.get( $filter_condition['species2_attributes']['species2_is_isnot'].strip(), '==' ) """$filter_condition['species2_attributes']['species2_attribute'].encode( 'string_escape' )""".decode( 'string_escape' ) ): + if not ( secondary_component.strand $is_isnot_valid.get( $filter_condition['species2_attributes']['species2_is_isnot'].value.strip(), '==' ) """$filter_condition['species2_attributes']['species2_attribute'].value.encode( 'string_escape' )""".decode( 'string_escape' ) ): return False #end if #end for

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[hg] galaxy 1722: Add a make_dict_copy method to Tool.execute so...
by Greg Von Kuster 26 Jan '09

26 Jan '09

details: http://www.bx.psu.edu/hg/galaxy/rev/2a81c4b95e20 changeset: 1722:2a81c4b95e20 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Mon Jan 26 14:41:00 2009 -0500 description: Add a make_dict_copy method to Tool.execute so that when wrapping the tool's inputs to display output labels and such, we are not overwriting the incoming param dictionary. Also, yet another fix for tranlsating EOL to so they can be displayed in the data.info in the histoy. 2 file(s) affected in this change: lib/galaxy/datatypes/data.py lib/galaxy/tools/actions/__init__.py diffs (77 lines): diff -r 9abb83ad372d -r 2a81c4b95e20 lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py Sat Jan 24 12:13:47 2009 -0500 +++ b/lib/galaxy/datatypes/data.py Mon Jan 26 14:41:00 2009 -0500 @@ -137,13 +137,14 @@ """Returns formatted html of dataset info""" try: # Change new line chars to html - if dataset.info.find( '\r\n' ) >= 0: - dataset.info = dataset.info.replace( '\r\n', ' ' ) - if dataset.info.find( '\r' ) >= 0: - dataset.info = dataset.info.replace( '\r', ' ' ) - if dataset.info.find( '\n' ) >= 0: - dataset.info = dataset.info.replace( '\n', ' ' ) - return escape( dataset.info ) + info = escape( dataset.info ) + if info.find( '\r\n' ) >= 0: + info = info.replace( '\r\n', ' ' ) + if info.find( '\r' ) >= 0: + info = info.replace( '\r', ' ' ) + if info.find( '\n' ) >= 0: + info = info.replace( '\n', ' ' ) + return info except: return "info unavailable" def validate(self, dataset): diff -r 9abb83ad372d -r 2a81c4b95e20 lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py Sat Jan 24 12:13:47 2009 -0500 +++ b/lib/galaxy/tools/actions/__init__.py Mon Jan 26 14:41:00 2009 -0500 @@ -6,6 +6,7 @@ from galaxy.web import url_for from galaxy.jobs import JOB_OK import galaxy.tools +from types import * import logging log = logging.getLogger( __name__ ) @@ -65,8 +66,21 @@ param_values[input.name] = input_datasets[ prefix + input.name ] tool.visit_inputs( param_values, visitor ) return input_datasets - + def execute(self, tool, trans, incoming={}, set_output_hid=True ): + def make_dict_copy( from_dict ): + """ + Makes a copy of input dictionary from_dict such that all values that are dictionaries + result in creation of a new dictionary ( a sort of deepcopy ). We may need to handle + other complex types ( e.g., lists, etc ), but not sure... + """ + copy_from_dict = {} + for key, value in from_dict.items(): + if type( value ).__name__ == 'dict': + copy_from_dict[ key ] = make_dict_copy( value ) + else: + copy_from_dict[ key ] = value + return copy_from_dict def wrap_values( inputs, input_values ): # Wrap tool inputs as necessary for input in inputs.itervalues(): @@ -75,7 +89,7 @@ wrap_values( input.inputs, d ) elif isinstance( input, Conditional ): values = input_values[ input.name ] - current = values["__current_case__"] + current = values[ "__current_case__" ] wrap_values( input.cases[current].inputs, values ) elif isinstance( input, DataToolParameter ): input_values[ input.name ] = \ @@ -172,7 +186,7 @@ data.blurb = "queued" # Set output label if output.label: - params = dict( incoming ) + params = make_dict_copy( incoming ) # wrapping the params allows the tool config to contain things like # <outputs> # <data format="input" name="output" label="Blat on ${<input_param>.name}" />

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[hg] galaxy 1721: Apparently I only committed these fixes to sec...
by Nate Coraor 24 Jan '09

24 Jan '09

details: http://www.bx.psu.edu/hg/galaxy/rev/9abb83ad372d changeset: 1721:9abb83ad372d user: Nate Coraor <nate(a)bx.psu.edu> date: Sat Jan 24 12:13:47 2009 -0500 description: Apparently I only committed these fixes to security. Recommit of changeset 2015:7a447128f2cd from security, Make UCSC build update scripts find elementtree properly 3 file(s) affected in this change: cron/parse_builds.py cron/parse_builds_3_sites.py cron/updateucsc.sh.sample diffs (55 lines): diff -r f27a815ae734 -r 9abb83ad372d cron/parse_builds.py --- a/cron/parse_builds.py Fri Jan 23 14:12:52 2009 -0500 +++ b/cron/parse_builds.py Sat Jan 24 12:13:47 2009 -0500 @@ -8,8 +8,12 @@ import sys import urllib -import pkg_resources; pkg_resources.require( "elementtree" ) -from elementtree import ElementTree +if sys.version_info[:2] >= ( 2, 5 ): + import xml.etree.ElementTree as ElementTree +else: + from galaxy import eggs + import pkg_resources; pkg_resources.require( "elementtree" ) + from elementtree import ElementTree URL = "http://genome-test.cse.ucsc.edu/cgi-bin/das/dsn" diff -r f27a815ae734 -r 9abb83ad372d cron/parse_builds_3_sites.py --- a/cron/parse_builds_3_sites.py Fri Jan 23 14:12:52 2009 -0500 +++ b/cron/parse_builds_3_sites.py Sat Jan 24 12:13:47 2009 -0500 @@ -5,8 +5,12 @@ import sys import urllib -import pkg_resources; pkg_resources.require( "elementtree" ) -from elementtree import ElementTree +if sys.version_info[:2] >= ( 2, 5 ): + import xml.etree.ElementTree as ElementTree +else: + from galaxy import eggs + import pkg_resources; pkg_resources.require( "elementtree" ) + from elementtree import ElementTree sites = ['http://genome.ucsc.edu/cgi-bin/', 'http://archaea.ucsc.edu/cgi-bin/', diff -r f27a815ae734 -r 9abb83ad372d cron/updateucsc.sh.sample --- a/cron/updateucsc.sh.sample Fri Jan 23 14:12:52 2009 -0500 +++ b/cron/updateucsc.sh.sample Sat Jan 24 12:13:47 2009 -0500 @@ -6,7 +6,7 @@ # Edit this line to refer to galaxy's path: GALAXY=/galaxy/path -export PYTHONPATH=${GALAXY}/modules:${GALAXY}/eggs:${GALAXY}/lib +export PYTHONPATH=${GALAXY}/lib # setup directories mkdir ${GALAXY}/tool-data/shared/ucsc/new @@ -57,4 +57,4 @@ echo "Manual addition was successful." else echo "Manual addition failed" >&2 -fi \ No newline at end of file +fi

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Alignment Extractors - in batch?
by Abhi Ratnakumar 23 Jan '09

23 Jan '09

Hello, I have multiple sequence alignment files in the *maf format, containing whole genome alignments from 6 species. I'm interested in extracting the sequence surrounding the exons of ~16,000 genes. I was wondering if it would be possible to run the Alignment Extractors tool in batch? Would it be possible for me to run it on the command line? Thanks ins Advance Abhi Ratnakumar By the way I'm a PhD student at Uppsala University, so any executables that you provide will be used for academic purposes only.

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[hg] galaxy 1720: in JobWrapper.fail(), save the traceback befor...
by Nate Coraor 23 Jan '09

23 Jan '09

details: http://www.bx.psu.edu/hg/galaxy/rev/f27a815ae734 changeset: 1720:f27a815ae734 user: Nate Coraor <nate(a)bx.psu.edu> date: Fri Jan 23 14:12:52 2009 -0500 description: in JobWrapper.fail(), save the traceback before doing anything else that might result in a traceback 1 file(s) affected in this change: lib/galaxy/jobs/__init__.py diffs (24 lines): diff -r 4fa4d0ddbf1f -r f27a815ae734 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py Fri Jan 23 12:55:35 2009 -0500 +++ b/lib/galaxy/jobs/__init__.py Fri Jan 23 14:12:52 2009 -0500 @@ -381,6 +381,10 @@ job.refresh() # if the job was deleted, don't fail it if not job.state == model.Job.states.DELETED: + # If the failure is due to a Galaxy framework exception, save the traceback + # Do this first in case we generate a traceback below + if exception: + job.traceback = traceback.format_exc() for dataset_assoc in job.output_datasets: if self.app.config.outputs_to_working_directory: false_path = os.path.abspath( os.path.join( self.working_directory, "galaxy_dataset_%d.dat" % dataset_assoc.dataset.dataset.id ) ) @@ -399,9 +403,6 @@ job.state = model.Job.states.ERROR job.command_line = self.command_line job.info = message - # If the failure is due to a Galaxy framework exception, save the traceback - if exception: - job.traceback = traceback.format_exc() job.flush() # If the job was deleted, just clean up self.cleanup()

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