diff --git a/tools/regVariation/best_regression_subsets.xml b/tools/regVariation/best_regression_subsets.xml index bf382f86cb7..84c3e3ddf3e 100644 --- a/tools/regVariation/best_regression_subsets.xml +++ b/tools/regVariation/best_regression_subsets.xml @@ -13,7 +13,9 @@ - + + + diff --git a/tools/regVariation/getIndels.py b/tools/regVariation/getIndels.py index 81bbb975038..d18b12e912c 100644 --- a/tools/regVariation/getIndels.py +++ b/tools/regVariation/getIndels.py @@ -1,7 +1,7 @@ #!/usr/bin/python """ -Estimate INDELs for pait-wise alignments. +Estimate INDELs for pair-wise alignments. usage: %prog maf_input out_file1 out_file2 """ @@ -10,22 +10,10 @@ from __future__ import division from galaxy import eggs import pkg_resources pkg_resources.require( "bx-python" ) -pkg_resources.require( "lrucache" ) -try: - pkg_resources.require("numpy") - pkg_resources.require( "python-lzo" ) -except: - pass +pkg_resources.require("numpy") import psyco_full import sys -import os, os.path -from UserDict import DictMixin -import bx.wiggle -from bx.binned_array import BinnedArray, FileBinnedArray -from bx.bitset import * -from bx.bitset_builders import * -from fpconst import isNaN from bx.cookbook import doc_optparse from galaxy.tools.exception_handling import * import bx.align.maf diff --git a/tools/regVariation/linear_regression.xml b/tools/regVariation/linear_regression.xml index d4fc74a1271..75c0da55556 100644 --- a/tools/regVariation/linear_regression.xml +++ b/tools/regVariation/linear_regression.xml @@ -12,7 +12,9 @@ - + + + diff --git a/tools/regVariation/quality_filter.py b/tools/regVariation/quality_filter.py index d77a296861d..9e0cb06a25f 100644 --- a/tools/regVariation/quality_filter.py +++ b/tools/regVariation/quality_filter.py @@ -12,11 +12,7 @@ from galaxy import eggs import pkg_resources pkg_resources.require( "bx-python" ) pkg_resources.require( "lrucache" ) -try: - pkg_resources.require("numpy") - pkg_resources.require( "python-lzo" ) -except: - pass +pkg_resources.require("numpy") import psyco_full import sys diff --git a/tools/regVariation/rcve.xml b/tools/regVariation/rcve.xml index 7fe82e92aca..1d1903cc114 100644 --- a/tools/regVariation/rcve.xml +++ b/tools/regVariation/rcve.xml @@ -11,7 +11,9 @@ - + + +