details: http://www.bx.psu.edu/hg/galaxy/rev/9f7d7e900cdf changeset: 3598:9f7d7e900cdf user: Kanwei Li <kanwei@gmail.com> date: Thu Apr 01 20:36:31 2010 -0400 description: Sync hashbangs diffstat: lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py | 2 +- lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py | 2 +- lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py | 2 +- scripts/check_eggs.py | 2 +- scripts/galaxy_messaging/server/daemon.py | 2 +- scripts/galaxy_messaging/server/data_transfer.py | 2 +- scripts/metagenomics/convert_title.py | 2 +- scripts/tools/re_escape_output.py | 2 +- tools/fasta_tools/fasta_compute_length.py | 2 +- tools/fasta_tools/fasta_concatenate_by_species.py | 2 +- tools/fasta_tools/fasta_filter_by_length.py | 2 +- tools/fasta_tools/fasta_to_tabular.py | 2 +- tools/metag_tools/blat_coverage_report.py | 2 +- tools/metag_tools/blat_mapping.py | 2 +- tools/metag_tools/blat_wrapper.py | 2 +- tools/metag_tools/convert_SOLiD_color2nuc.py | 2 +- tools/metag_tools/fastqsolexa_to_fasta_qual.py | 2 +- tools/metag_tools/mapping_to_ucsc.py | 2 +- tools/metag_tools/megablast_wrapper.py | 2 +- tools/metag_tools/megablast_xml_parser.py | 2 +- tools/metag_tools/rmap_wrapper.py | 2 +- tools/metag_tools/rmapq_wrapper.py | 2 +- tools/metag_tools/short_reads_figure_high_quality_length.py | 2 +- tools/metag_tools/short_reads_figure_score.py | 2 +- tools/metag_tools/short_reads_trim_seq.py | 2 +- tools/metag_tools/shrimp_color_wrapper.py | 2 +- tools/metag_tools/shrimp_wrapper.py | 2 +- tools/metag_tools/split_paired_reads.py | 2 +- tools/new_operations/get_flanks.py | 2 +- tools/next_gen_conversion/fastq_conversions.py | 2 +- tools/next_gen_conversion/solid_to_fastq.py | 2 +- tools/regVariation/getIndels.py | 2 +- tools/regVariation/maf_cpg_filter.py | 2 +- tools/regVariation/quality_filter.py | 2 +- tools/regVariation/substitution_rates.py | 2 +- tools/regVariation/substitutions.py | 2 +- tools/regVariation/windowSplitter.py | 2 +- tools/samtools/pileup_interval.py | 2 +- tools/samtools/sam_merge.py | 2 +- tools/samtools/sam_pileup.py | 2 +- tools/samtools/sam_to_bam.py | 2 +- tools/solid_tools/maq_cs_wrapper.py | 2 +- tools/solid_tools/solid_qual_stats.py | 2 +- tools/sr_mapping/bowtie_wrapper.py | 2 +- tools/sr_mapping/bwa_wrapper.py | 2 +- tools/sr_mapping/lastz_paired_reads_wrapper.py | 2 +- tools/sr_mapping/lastz_wrapper.py | 2 +- tools/stats/gsummary.py | 2 +- tools/tophat/tophat_wrapper.py | 2 +- 49 files changed, 49 insertions(+), 49 deletions(-) diffs (441 lines): diff -r 8457a6f3214a -r 9f7d7e900cdf lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py --- a/lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py Thu Apr 01 16:02:19 2010 -0400 +++ b/lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py Thu Apr 01 20:36:31 2010 -0400 @@ -1,4 +1,4 @@ -#! /usr/bin/python +#!/usr/bin/env python # This code exists in 2 places: ~/datatypes/converters and ~/tools/fasta_tools """ Input: fasta, minimal length, maximal length diff -r 8457a6f3214a -r 9f7d7e900cdf lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py --- a/lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py Thu Apr 01 16:02:19 2010 -0400 +++ b/lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py Thu Apr 01 20:36:31 2010 -0400 @@ -1,4 +1,4 @@ -#! /usr/bin/python +#!/usr/bin/env python """ convert fastqsolexa file to separated sequence and quality files. diff -r 8457a6f3214a -r 9f7d7e900cdf lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py --- a/lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py Thu Apr 01 16:02:19 2010 -0400 +++ b/lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py Thu Apr 01 20:36:31 2010 -0400 @@ -1,4 +1,4 @@ -#! /usr/bin/python +#!/usr/bin/env python """ convert fastqsolexa file to separated sequence and quality files. diff -r 8457a6f3214a -r 9f7d7e900cdf scripts/check_eggs.py --- a/scripts/check_eggs.py Thu Apr 01 16:02:19 2010 -0400 +++ b/scripts/check_eggs.py Thu Apr 01 20:36:31 2010 -0400 @@ -1,4 +1,4 @@ -#! /usr/bin/python +#!/usr/bin/env python """ usage: check_eggs.py """ diff -r 8457a6f3214a -r 9f7d7e900cdf scripts/galaxy_messaging/server/daemon.py --- a/scripts/galaxy_messaging/server/daemon.py Thu Apr 01 16:02:19 2010 -0400 +++ b/scripts/galaxy_messaging/server/daemon.py Thu Apr 01 20:36:31 2010 -0400 @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/env python """ Data Transfer Script Daemon diff -r 8457a6f3214a -r 9f7d7e900cdf scripts/galaxy_messaging/server/data_transfer.py --- a/scripts/galaxy_messaging/server/data_transfer.py Thu Apr 01 16:02:19 2010 -0400 +++ b/scripts/galaxy_messaging/server/data_transfer.py Thu Apr 01 20:36:31 2010 -0400 @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/env python """ Data Transfer Script: Sequencer to Galaxy diff -r 8457a6f3214a -r 9f7d7e900cdf scripts/metagenomics/convert_title.py --- a/scripts/metagenomics/convert_title.py Thu Apr 01 16:02:19 2010 -0400 +++ b/scripts/metagenomics/convert_title.py Thu Apr 01 20:36:31 2010 -0400 @@ -1,4 +1,4 @@ -#! /usr/bin/python +#!/usr/bin/env python """ convert nt and wgs data (fasta format) to giNumber_seqLen diff -r 8457a6f3214a -r 9f7d7e900cdf scripts/tools/re_escape_output.py --- a/scripts/tools/re_escape_output.py Thu Apr 01 16:02:19 2010 -0400 +++ b/scripts/tools/re_escape_output.py Thu Apr 01 20:36:31 2010 -0400 @@ -1,4 +1,4 @@ -#! /usr/bin/python +#!/usr/bin/env python """ Escapes a file into a form suitable for use with tool tests using re_match or re_match_multiline (when -m/--multiline option is used) diff -r 8457a6f3214a -r 9f7d7e900cdf tools/fasta_tools/fasta_compute_length.py --- a/tools/fasta_tools/fasta_compute_length.py Thu Apr 01 16:02:19 2010 -0400 +++ b/tools/fasta_tools/fasta_compute_length.py Thu Apr 01 20:36:31 2010 -0400 @@ -1,4 +1,4 @@ -#! /usr/bin/python +#!/usr/bin/env python """ Input: fasta, int Output: tabular diff -r 8457a6f3214a -r 9f7d7e900cdf tools/fasta_tools/fasta_concatenate_by_species.py --- a/tools/fasta_tools/fasta_concatenate_by_species.py Thu Apr 01 16:02:19 2010 -0400 +++ b/tools/fasta_tools/fasta_concatenate_by_species.py Thu Apr 01 20:36:31 2010 -0400 @@ -1,4 +1,4 @@ -#! /usr/bin/python +#!/usr/bin/env python #Dan Blankenberg """ Takes a Multiple Alignment FASTA file and concatenates diff -r 8457a6f3214a -r 9f7d7e900cdf tools/fasta_tools/fasta_filter_by_length.py --- a/tools/fasta_tools/fasta_filter_by_length.py Thu Apr 01 16:02:19 2010 -0400 +++ b/tools/fasta_tools/fasta_filter_by_length.py Thu Apr 01 20:36:31 2010 -0400 @@ -1,4 +1,4 @@ -#! /usr/bin/python +#!/usr/bin/env python """ Input: fasta, minimal length, maximal length Output: fasta diff -r 8457a6f3214a -r 9f7d7e900cdf tools/fasta_tools/fasta_to_tabular.py --- a/tools/fasta_tools/fasta_to_tabular.py Thu Apr 01 16:02:19 2010 -0400 +++ b/tools/fasta_tools/fasta_to_tabular.py Thu Apr 01 20:36:31 2010 -0400 @@ -1,4 +1,4 @@ -#! /usr/bin/python +#!/usr/bin/env python # This code exists in 2 places: ~/datatypes/converters and ~/tools/fasta_tools """ Input: fasta, int diff -r 8457a6f3214a -r 9f7d7e900cdf tools/metag_tools/blat_coverage_report.py --- a/tools/metag_tools/blat_coverage_report.py Thu Apr 01 16:02:19 2010 -0400 +++ b/tools/metag_tools/blat_coverage_report.py Thu Apr 01 20:36:31 2010 -0400 @@ -1,4 +1,4 @@ -#! /usr/bin/python +#!/usr/bin/env python import os, sys diff -r 8457a6f3214a -r 9f7d7e900cdf tools/metag_tools/blat_mapping.py --- a/tools/metag_tools/blat_mapping.py Thu Apr 01 16:02:19 2010 -0400 +++ b/tools/metag_tools/blat_mapping.py Thu Apr 01 20:36:31 2010 -0400 @@ -1,4 +1,4 @@ -#! /usr/bin/python +#!/usr/bin/env python import os, sys diff -r 8457a6f3214a -r 9f7d7e900cdf tools/metag_tools/blat_wrapper.py --- a/tools/metag_tools/blat_wrapper.py Thu Apr 01 16:02:19 2010 -0400 +++ b/tools/metag_tools/blat_wrapper.py Thu Apr 01 20:36:31 2010 -0400 @@ -1,4 +1,4 @@ -#! /usr/bin/python +#!/usr/bin/env python import os, sys, tempfile diff -r 8457a6f3214a -r 9f7d7e900cdf tools/metag_tools/convert_SOLiD_color2nuc.py --- a/tools/metag_tools/convert_SOLiD_color2nuc.py Thu Apr 01 16:02:19 2010 -0400 +++ b/tools/metag_tools/convert_SOLiD_color2nuc.py Thu Apr 01 20:36:31 2010 -0400 @@ -1,4 +1,4 @@ -#! /usr/bin/python +#!/usr/bin/env python """ convert SOLiD calor-base data to nucleotide sequence example: T011213122200221123032111221021210131332222101 diff -r 8457a6f3214a -r 9f7d7e900cdf tools/metag_tools/fastqsolexa_to_fasta_qual.py --- a/tools/metag_tools/fastqsolexa_to_fasta_qual.py Thu Apr 01 16:02:19 2010 -0400 +++ b/tools/metag_tools/fastqsolexa_to_fasta_qual.py Thu Apr 01 20:36:31 2010 -0400 @@ -1,4 +1,4 @@ -#! /usr/bin/python +#!/usr/bin/env python """ convert fastqsolexa file to separated sequence and quality files. diff -r 8457a6f3214a -r 9f7d7e900cdf tools/metag_tools/mapping_to_ucsc.py --- a/tools/metag_tools/mapping_to_ucsc.py Thu Apr 01 16:02:19 2010 -0400 +++ b/tools/metag_tools/mapping_to_ucsc.py Thu Apr 01 20:36:31 2010 -0400 @@ -1,4 +1,4 @@ -#! /usr/bin/python +#!/usr/bin/env python from galaxy import eggs import sys, tempfile, os diff -r 8457a6f3214a -r 9f7d7e900cdf tools/metag_tools/megablast_wrapper.py --- a/tools/metag_tools/megablast_wrapper.py Thu Apr 01 16:02:19 2010 -0400 +++ b/tools/metag_tools/megablast_wrapper.py Thu Apr 01 20:36:31 2010 -0400 @@ -1,4 +1,4 @@ -#! /usr/bin/python +#!/usr/bin/env python """ run megablast for metagenomics data diff -r 8457a6f3214a -r 9f7d7e900cdf tools/metag_tools/megablast_xml_parser.py --- a/tools/metag_tools/megablast_xml_parser.py Thu Apr 01 16:02:19 2010 -0400 +++ b/tools/metag_tools/megablast_xml_parser.py Thu Apr 01 20:36:31 2010 -0400 @@ -1,4 +1,4 @@ -#! /usr/bin/python +#!/usr/bin/env python import sys, os, re diff -r 8457a6f3214a -r 9f7d7e900cdf tools/metag_tools/rmap_wrapper.py --- a/tools/metag_tools/rmap_wrapper.py Thu Apr 01 16:02:19 2010 -0400 +++ b/tools/metag_tools/rmap_wrapper.py Thu Apr 01 20:36:31 2010 -0400 @@ -1,4 +1,4 @@ -#! /usr/bin/python +#!/usr/bin/env python import os, sys, tempfile diff -r 8457a6f3214a -r 9f7d7e900cdf tools/metag_tools/rmapq_wrapper.py --- a/tools/metag_tools/rmapq_wrapper.py Thu Apr 01 16:02:19 2010 -0400 +++ b/tools/metag_tools/rmapq_wrapper.py Thu Apr 01 20:36:31 2010 -0400 @@ -1,4 +1,4 @@ -#! /usr/bin/python +#!/usr/bin/env python import os, sys, tempfile diff -r 8457a6f3214a -r 9f7d7e900cdf tools/metag_tools/short_reads_figure_high_quality_length.py --- a/tools/metag_tools/short_reads_figure_high_quality_length.py Thu Apr 01 16:02:19 2010 -0400 +++ b/tools/metag_tools/short_reads_figure_high_quality_length.py Thu Apr 01 20:36:31 2010 -0400 @@ -1,4 +1,4 @@ -#! /usr/bin/python +#!/usr/bin/env python import os, sys, math, tempfile, zipfile, re from rpy import * diff -r 8457a6f3214a -r 9f7d7e900cdf tools/metag_tools/short_reads_figure_score.py --- a/tools/metag_tools/short_reads_figure_score.py Thu Apr 01 16:02:19 2010 -0400 +++ b/tools/metag_tools/short_reads_figure_score.py Thu Apr 01 20:36:31 2010 -0400 @@ -1,4 +1,4 @@ -#! /usr/bin/python +#!/usr/bin/env python """ boxplot: - box: first quartile and third quartile diff -r 8457a6f3214a -r 9f7d7e900cdf tools/metag_tools/short_reads_trim_seq.py --- a/tools/metag_tools/short_reads_trim_seq.py Thu Apr 01 16:02:19 2010 -0400 +++ b/tools/metag_tools/short_reads_trim_seq.py Thu Apr 01 20:36:31 2010 -0400 @@ -1,4 +1,4 @@ -#! /usr/bin/python +#!/usr/bin/env python """ trim reads based on the quality scores input: read file and quality score file diff -r 8457a6f3214a -r 9f7d7e900cdf tools/metag_tools/shrimp_color_wrapper.py --- a/tools/metag_tools/shrimp_color_wrapper.py Thu Apr 01 16:02:19 2010 -0400 +++ b/tools/metag_tools/shrimp_color_wrapper.py Thu Apr 01 20:36:31 2010 -0400 @@ -1,4 +1,4 @@ -#! /usr/bin/python +#!/usr/bin/env python """ SHRiMP wrapper : Color space diff -r 8457a6f3214a -r 9f7d7e900cdf tools/metag_tools/shrimp_wrapper.py --- a/tools/metag_tools/shrimp_wrapper.py Thu Apr 01 16:02:19 2010 -0400 +++ b/tools/metag_tools/shrimp_wrapper.py Thu Apr 01 20:36:31 2010 -0400 @@ -1,4 +1,4 @@ -#! /usr/bin/python +#!/usr/bin/env python """ TODO diff -r 8457a6f3214a -r 9f7d7e900cdf tools/metag_tools/split_paired_reads.py --- a/tools/metag_tools/split_paired_reads.py Thu Apr 01 16:02:19 2010 -0400 +++ b/tools/metag_tools/split_paired_reads.py Thu Apr 01 20:36:31 2010 -0400 @@ -1,4 +1,4 @@ -#! /usr/bin/python +#!/usr/bin/env python """ Split fixed length paired end reads diff -r 8457a6f3214a -r 9f7d7e900cdf tools/new_operations/get_flanks.py --- a/tools/new_operations/get_flanks.py Thu Apr 01 16:02:19 2010 -0400 +++ b/tools/new_operations/get_flanks.py Thu Apr 01 20:36:31 2010 -0400 @@ -1,4 +1,4 @@ -#! /usr/bin/python +#!/usr/bin/env python #Done by: Guru """ diff -r 8457a6f3214a -r 9f7d7e900cdf tools/next_gen_conversion/fastq_conversions.py --- a/tools/next_gen_conversion/fastq_conversions.py Thu Apr 01 16:02:19 2010 -0400 +++ b/tools/next_gen_conversion/fastq_conversions.py Thu Apr 01 20:36:31 2010 -0400 @@ -1,4 +1,4 @@ -#! /usr/bin/python +#!/usr/bin/env python """ Performs various conversions around Sanger FASTQ data diff -r 8457a6f3214a -r 9f7d7e900cdf tools/next_gen_conversion/solid_to_fastq.py --- a/tools/next_gen_conversion/solid_to_fastq.py Thu Apr 01 16:02:19 2010 -0400 +++ b/tools/next_gen_conversion/solid_to_fastq.py Thu Apr 01 20:36:31 2010 -0400 @@ -1,4 +1,4 @@ -#! /usr/bin/python +#!/usr/bin/env python """ Converts SOLiD data to Sanger FASTQ format. diff -r 8457a6f3214a -r 9f7d7e900cdf tools/regVariation/getIndels.py --- a/tools/regVariation/getIndels.py Thu Apr 01 16:02:19 2010 -0400 +++ b/tools/regVariation/getIndels.py Thu Apr 01 20:36:31 2010 -0400 @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/env python """ Estimate INDELs for pair-wise alignments. diff -r 8457a6f3214a -r 9f7d7e900cdf tools/regVariation/maf_cpg_filter.py --- a/tools/regVariation/maf_cpg_filter.py Thu Apr 01 16:02:19 2010 -0400 +++ b/tools/regVariation/maf_cpg_filter.py Thu Apr 01 20:36:31 2010 -0400 @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/env python #Guruprasad Ananda #Adapted from bx/scripts/maf_mask_cpg.py """ diff -r 8457a6f3214a -r 9f7d7e900cdf tools/regVariation/quality_filter.py --- a/tools/regVariation/quality_filter.py Thu Apr 01 16:02:19 2010 -0400 +++ b/tools/regVariation/quality_filter.py Thu Apr 01 20:36:31 2010 -0400 @@ -1,4 +1,4 @@ -#! /usr/bin/python +#!/usr/bin/env python #Guruprasad Ananda """ Filter based on nucleotide quality (PHRED score). diff -r 8457a6f3214a -r 9f7d7e900cdf tools/regVariation/substitution_rates.py --- a/tools/regVariation/substitution_rates.py Thu Apr 01 16:02:19 2010 -0400 +++ b/tools/regVariation/substitution_rates.py Thu Apr 01 20:36:31 2010 -0400 @@ -1,4 +1,4 @@ -#! /usr/bin/python +#!/usr/bin/env python #guruprasad Ananda """ Estimates substitution rates from pairwise alignments using JC69 model. diff -r 8457a6f3214a -r 9f7d7e900cdf tools/regVariation/substitutions.py --- a/tools/regVariation/substitutions.py Thu Apr 01 16:02:19 2010 -0400 +++ b/tools/regVariation/substitutions.py Thu Apr 01 20:36:31 2010 -0400 @@ -1,4 +1,4 @@ -#! /usr/bin/python +#!/usr/bin/env python #Guruprasad ANanda """ Fetches substitutions from pairwise alignments. diff -r 8457a6f3214a -r 9f7d7e900cdf tools/regVariation/windowSplitter.py --- a/tools/regVariation/windowSplitter.py Thu Apr 01 16:02:19 2010 -0400 +++ b/tools/regVariation/windowSplitter.py Thu Apr 01 20:36:31 2010 -0400 @@ -1,4 +1,4 @@ -#! /usr/bin/python +#!/usr/bin/env python """ Split into windows. diff -r 8457a6f3214a -r 9f7d7e900cdf tools/samtools/pileup_interval.py --- a/tools/samtools/pileup_interval.py Thu Apr 01 16:02:19 2010 -0400 +++ b/tools/samtools/pileup_interval.py Thu Apr 01 20:36:31 2010 -0400 @@ -1,4 +1,4 @@ -#! /usr/bin/python +#!/usr/bin/env python """ Condenses pileup format into ranges of bases. diff -r 8457a6f3214a -r 9f7d7e900cdf tools/samtools/sam_merge.py --- a/tools/samtools/sam_merge.py Thu Apr 01 16:02:19 2010 -0400 +++ b/tools/samtools/sam_merge.py Thu Apr 01 20:36:31 2010 -0400 @@ -1,4 +1,4 @@ -#! /usr/bin/python +#!/usr/bin/env python """ Merges any number of BAM files diff -r 8457a6f3214a -r 9f7d7e900cdf tools/samtools/sam_pileup.py --- a/tools/samtools/sam_pileup.py Thu Apr 01 16:02:19 2010 -0400 +++ b/tools/samtools/sam_pileup.py Thu Apr 01 20:36:31 2010 -0400 @@ -1,4 +1,4 @@ -#! /usr/bin/python +#!/usr/bin/env python """ Creates a pileup file from a bam file and a reference. diff -r 8457a6f3214a -r 9f7d7e900cdf tools/samtools/sam_to_bam.py --- a/tools/samtools/sam_to_bam.py Thu Apr 01 16:02:19 2010 -0400 +++ b/tools/samtools/sam_to_bam.py Thu Apr 01 20:36:31 2010 -0400 @@ -1,4 +1,4 @@ -#! /usr/bin/python +#!/usr/bin/env python """ Converts SAM data to sorted BAM data. usage: sam_to_bam.py [options] diff -r 8457a6f3214a -r 9f7d7e900cdf tools/solid_tools/maq_cs_wrapper.py --- a/tools/solid_tools/maq_cs_wrapper.py Thu Apr 01 16:02:19 2010 -0400 +++ b/tools/solid_tools/maq_cs_wrapper.py Thu Apr 01 20:36:31 2010 -0400 @@ -1,4 +1,4 @@ -#! /usr/bin/python +#!/usr/bin/env python #Guruprasad Ananda #MAQ mapper for SOLiD colourspace-reads diff -r 8457a6f3214a -r 9f7d7e900cdf tools/solid_tools/solid_qual_stats.py --- a/tools/solid_tools/solid_qual_stats.py Thu Apr 01 16:02:19 2010 -0400 +++ b/tools/solid_tools/solid_qual_stats.py Thu Apr 01 20:36:31 2010 -0400 @@ -1,4 +1,4 @@ -#! /usr/bin/python +#!/usr/bin/env python #Guruprasad Ananda import sys, os, zipfile, tempfile diff -r 8457a6f3214a -r 9f7d7e900cdf tools/sr_mapping/bowtie_wrapper.py --- a/tools/sr_mapping/bowtie_wrapper.py Thu Apr 01 16:02:19 2010 -0400 +++ b/tools/sr_mapping/bowtie_wrapper.py Thu Apr 01 20:36:31 2010 -0400 @@ -1,4 +1,4 @@ -#! /usr/bin/python +#!/usr/bin/env python """ Runs Bowtie on single-end or paired-end data. diff -r 8457a6f3214a -r 9f7d7e900cdf tools/sr_mapping/bwa_wrapper.py --- a/tools/sr_mapping/bwa_wrapper.py Thu Apr 01 16:02:19 2010 -0400 +++ b/tools/sr_mapping/bwa_wrapper.py Thu Apr 01 20:36:31 2010 -0400 @@ -1,4 +1,4 @@ -#! /usr/bin/python +#!/usr/bin/env python """ Runs BWA on single-end or paired-end data. diff -r 8457a6f3214a -r 9f7d7e900cdf tools/sr_mapping/lastz_paired_reads_wrapper.py --- a/tools/sr_mapping/lastz_paired_reads_wrapper.py Thu Apr 01 16:02:19 2010 -0400 +++ b/tools/sr_mapping/lastz_paired_reads_wrapper.py Thu Apr 01 20:36:31 2010 -0400 @@ -1,4 +1,4 @@ -#! /usr/bin/python +#!/usr/bin/env python """ Runs Lastz paired read alignment process diff -r 8457a6f3214a -r 9f7d7e900cdf tools/sr_mapping/lastz_wrapper.py --- a/tools/sr_mapping/lastz_wrapper.py Thu Apr 01 16:02:19 2010 -0400 +++ b/tools/sr_mapping/lastz_wrapper.py Thu Apr 01 20:36:31 2010 -0400 @@ -1,4 +1,4 @@ -#! /usr/bin/python +#!/usr/bin/env python """ Runs Lastz diff -r 8457a6f3214a -r 9f7d7e900cdf tools/stats/gsummary.py --- a/tools/stats/gsummary.py Thu Apr 01 16:02:19 2010 -0400 +++ b/tools/stats/gsummary.py Thu Apr 01 20:36:31 2010 -0400 @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/env python import sys, re, tempfile from rpy import * diff -r 8457a6f3214a -r 9f7d7e900cdf tools/tophat/tophat_wrapper.py --- a/tools/tophat/tophat_wrapper.py Thu Apr 01 16:02:19 2010 -0400 +++ b/tools/tophat/tophat_wrapper.py Thu Apr 01 20:36:31 2010 -0400 @@ -1,4 +1,4 @@ -#! /usr/bin/python +#!/usr/bin/env python import optparse, os, shutil, sys, tempfile