details: http://www.bx.psu.edu/hg/galaxy/rev/a4214de3752e changeset: 1733:a4214de3752e user: guru date: Tue Feb 03 18:34:27 2009 -0500 description: Fixes to get functional tests working. 4 file(s) affected in this change: test-data/branchlength_out.dat tools/hyphy/hyphy_branch_lengths_wrapper.xml tools/regVariation/getIndels.py tools/regVariation/quality_filter.py diffs (95 lines): diff -r 4d4de72c57c8 -r a4214de3752e test-data/branchlength_out.dat --- a/test-data/branchlength_out.dat Tue Feb 03 15:06:21 2009 -0500 +++ b/test-data/branchlength_out.dat Tue Feb 03 18:34:27 2009 -0500 @@ -7,27 +7,27 @@ 1 Node4 4.93827e-31 0 0.23542 1 canFam1.chr14(+):42826409-42826418|canFam1_0 4.93827e-31 0 0.23542 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 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 1.76058e-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 1.27931e-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 0 0 0.143452 -3 canFam1.chr14(+):42826434-42826446|canFam1_2 1.70011e-31 0 0.143452 -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 +2 hg17.chr7(+):26907310-26907326|hg17_1 1.90313e-31 0 0.13592 +2 panTro1.chr6(+):28037328-28037344|panTro1_1 1.90313e-31 0 0.13592 +2 Node1 4.10285e-19 0 0.13592 +2 mm5.chr6(+):52104031-52104047|mm5_1 2.02063e-19 0 0.13592 +2 rn3.chr4(+):80734404-80734420|rn3_1 0.069102 0.00372954 0.421893 +2 Node4 1.90313e-31 0 0.13592 +2 canFam1.chr14(+):42826418-42826434|canFam1_1 1.13513e-19 0 0.13592 +2 Total Tree 0.069102 0.00372954 0.421893 +3 hg17.chr7(+):26907326-26907338|hg17_2 8.84162e-30 0 0.167446 +3 panTro1.chr6(+):28037344-28037356|panTro1_2 8.84162e-30 0 0.167446 +3 Node1 0 0 0.167446 +3 mm5.chr6(+):52104047-52104059|mm5_2 0 0 0.24858 +3 rn3.chr4(+):80734420-80734432|rn3_2 0.201494 0.0309976 0.7364 +3 Node4 0.31691 0.0691821 1.08477 +3 canFam1.chr14(+):42826434-42826446|canFam1_2 0 0 0.167446 +3 Total Tree 0.518404 0.168855 1.26753 +4 hg17.chr7(+):26907338-26907654|hg17_3 1.11429e-19 0 0.0061265 +4 panTro1.chr6(+):28037356-28037672|panTro1_3 1.11866e-19 0 0.0061265 +4 Node1 0.0583134 0.0318643 0.0951333 +4 mm5.chr6(+):52104059-52104375|mm5_3 0.0357704 0.0167845 0.0644066 +4 rn3.chr4(+):80734432-80734748|rn3_3 0.0320354 0.0141331 0.0594834 +4 Node4 0.0770295 0.0463471 0.11848 +4 canFam1.chr14(+):42826446-42826762|canFam1_3 0.0575307 0.0316345 0.0936592 +4 Total Tree 0.260679 0.205255 0.325684 diff -r 4d4de72c57c8 -r a4214de3752e tools/hyphy/hyphy_branch_lengths_wrapper.xml --- a/tools/hyphy/hyphy_branch_lengths_wrapper.xml Tue Feb 03 15:06:21 2009 -0500 +++ b/tools/hyphy/hyphy_branch_lengths_wrapper.xml Tue Feb 03 18:34:27 2009 -0500 @@ -1,4 +1,4 @@ -<?xml version="1.1.0"?> +<?xml version="1.2.0"?> <tool name="Branch Lengths" id="hyphy_branch_lengths_wrapper1"> <description>Estimation</description> diff -r 4d4de72c57c8 -r a4214de3752e tools/regVariation/getIndels.py --- a/tools/regVariation/getIndels.py Tue Feb 03 15:06:21 2009 -0500 +++ b/tools/regVariation/getIndels.py Tue Feb 03 18:34:27 2009 -0500 @@ -10,8 +10,10 @@ from galaxy import eggs import pkg_resources pkg_resources.require( "bx-python" ) -pkg_resources.require("numpy") - +try: + pkg_resources.require("numpy") +except: + pass import psyco_full import sys from bx.cookbook import doc_optparse diff -r 4d4de72c57c8 -r a4214de3752e tools/regVariation/quality_filter.py --- a/tools/regVariation/quality_filter.py Tue Feb 03 15:06:21 2009 -0500 +++ b/tools/regVariation/quality_filter.py Tue Feb 03 18:34:27 2009 -0500 @@ -12,7 +12,10 @@ import pkg_resources pkg_resources.require( "bx-python" ) pkg_resources.require( "lrucache" ) -pkg_resources.require("numpy") +try: + pkg_resources.require("numpy") +except: + pass import psyco_full import sys