# HG changeset patch # User scisjnu123 # Date 1570192144 14400 # Node ID aba80e38756a775eda911013629dcef9e5786d04 # Parent 5f1b354dc002377a42fb0527c110e33028e8c965 Deleted selected files diff -r 5f1b354dc002 -r aba80e38756a samtools/data_manager_sam_fasta_index_builder/2a1ac1abc3f7/data_manager_sam_fasta_index_builder/README --- a/samtools/data_manager_sam_fasta_index_builder/2a1ac1abc3f7/data_manager_sam_fasta_index_builder/README Fri Oct 04 08:07:15 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -TODO diff -r 5f1b354dc002 -r aba80e38756a samtools/data_manager_sam_fasta_index_builder/2a1ac1abc3f7/data_manager_sam_fasta_index_builder/data_manager/data_manager_sam_fasta_index_builder.py --- a/samtools/data_manager_sam_fasta_index_builder/2a1ac1abc3f7/data_manager_sam_fasta_index_builder/data_manager/data_manager_sam_fasta_index_builder.py Fri Oct 04 08:07:15 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,87 +0,0 @@ -#!/usr/bin/env python -#Dan Blankenberg - -import json -import optparse -import os -import subprocess -import sys -import tempfile - -CHUNK_SIZE = 2**20 - -DEFAULT_DATA_TABLE_NAME = "fasta_indexes" - -def get_id_name( params, dbkey, fasta_description=None): - #TODO: ensure sequence_id is unique and does not already appear in location file - sequence_id = params['param_dict']['sequence_id'] - if not sequence_id: - sequence_id = dbkey - - sequence_name = params['param_dict']['sequence_name'] - if not sequence_name: - sequence_name = fasta_description - if not sequence_name: - sequence_name = dbkey - return sequence_id, sequence_name - -def build_sam_index( data_manager_dict, fasta_filename, target_directory, dbkey, sequence_id, sequence_name, data_table_name=DEFAULT_DATA_TABLE_NAME ): - #TODO: allow multiple FASTA input files - assert os.path.exists( fasta_filename ), 'FASTA file "%s" is missing, cannot build samtools index.' % fasta_filename - fasta_base_name = os.path.split( fasta_filename )[-1] - sym_linked_fasta_filename = os.path.join( target_directory, fasta_base_name ) - os.symlink( fasta_filename, sym_linked_fasta_filename ) - - args = [ 'samtools', 'faidx' ] - args.append( sym_linked_fasta_filename ) - tmp_stderr = tempfile.NamedTemporaryFile( prefix = "tmp-data-manager-sam_fa_index_builder-stderr" ) - proc = subprocess.Popen( args=args, shell=False, cwd=target_directory, stderr=tmp_stderr.fileno() ) - return_code = proc.wait() - if return_code: - tmp_stderr.flush() - tmp_stderr.seek( 0 ) - sys.stderr.write( "Error building index:\n" ) - while True: - chunk = tmp_stderr.read( CHUNK_SIZE ) - if not chunk: - break - sys.stderr.write( chunk ) - sys.exit( return_code ) - tmp_stderr.close() - data_table_entry = dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_name ) - _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ) - -def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ): - data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} ) - data_manager_dict['data_tables'][ data_table_name ] = data_manager_dict['data_tables'].get( data_table_name, [] ) - data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry ) - return data_manager_dict - -def main(): - #Parse Command Line - parser = optparse.OptionParser() - parser.add_option( '-f', '--fasta_filename', dest='fasta_filename', action='store', type="string", default=None, help='fasta_filename' ) - parser.add_option( '-d', '--fasta_dbkey', dest='fasta_dbkey', action='store', type="string", default=None, help='fasta_dbkey' ) - parser.add_option( '-t', '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='fasta_description' ) - parser.add_option( '-n', '--data_table_name', dest='data_table_name', action='store', type="string", default=None, help='data_table_name' ) - (options, args) = parser.parse_args() - - filename = args[0] - - params = json.loads( open( filename ).read() ) - target_directory = params[ 'output_data' ][0]['extra_files_path'] - os.mkdir( target_directory ) - data_manager_dict = {} - - if options.fasta_dbkey in [ None, '', '?' ]: - raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( options.fasta_dbkey ) ) - - sequence_id, sequence_name = get_id_name( params, dbkey=options.fasta_dbkey, fasta_description=options.fasta_description ) - - #build the index - build_sam_index( data_manager_dict, options.fasta_filename, target_directory, options.fasta_dbkey, sequence_id, sequence_name, data_table_name=options.data_table_name or DEFAULT_DATA_TABLE_NAME ) - - #save info to json file - open( filename, 'wb' ).write( json.dumps( data_manager_dict ) ) - -if __name__ == "__main__": main() diff -r 5f1b354dc002 -r aba80e38756a samtools/data_manager_sam_fasta_index_builder/2a1ac1abc3f7/data_manager_sam_fasta_index_builder/data_manager/data_manager_sam_fasta_index_builder.xml --- a/samtools/data_manager_sam_fasta_index_builder/2a1ac1abc3f7/data_manager_sam_fasta_index_builder/data_manager/data_manager_sam_fasta_index_builder.xml Fri Oct 04 08:07:15 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,25 +0,0 @@ - - builder - - samtools - - data_manager_sam_fasta_index_builder.py "${out_file}" --fasta_filename "${all_fasta_source.fields.path}" --fasta_dbkey "${all_fasta_source.fields.dbkey}" --fasta_description "${all_fasta_source.fields.name}" --data_table_name "fasta_indexes" - - - - - - - - - - - - - -.. class:: infomark - -**Notice:** If you leave name, description, or id blank, it will be generated automatically. - - - diff -r 5f1b354dc002 -r aba80e38756a samtools/data_manager_sam_fasta_index_builder/2a1ac1abc3f7/data_manager_sam_fasta_index_builder/data_manager_conf.xml --- a/samtools/data_manager_sam_fasta_index_builder/2a1ac1abc3f7/data_manager_sam_fasta_index_builder/data_manager_conf.xml Fri Oct 04 08:07:15 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,22 +0,0 @@ - - - - - - - - - - - - - ${dbkey}/sam_indexes/${value} - - ${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/sam_indexes/${value}/${path} - abspath - - - - - - diff -r 5f1b354dc002 -r aba80e38756a samtools/data_manager_sam_fasta_index_builder/2a1ac1abc3f7/data_manager_sam_fasta_index_builder/tool-data/all_fasta.loc.sample --- a/samtools/data_manager_sam_fasta_index_builder/2a1ac1abc3f7/data_manager_sam_fasta_index_builder/tool-data/all_fasta.loc.sample Fri Oct 04 08:07:15 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,18 +0,0 @@ -#This file lists the locations and dbkeys of all the fasta files -#under the "genome" directory (a directory that contains a directory -#for each build). The script extract_fasta.py will generate the file -#all_fasta.loc. This file has the format (white space characters are -#TAB characters): -# -# -# -#So, all_fasta.loc could look something like this: -# -#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa -#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa -#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa -# -#Your all_fasta.loc file should contain an entry for each individual -#fasta file. So there will be multiple fasta files for each build, -#such as with hg19 above. -# diff -r 5f1b354dc002 -r aba80e38756a samtools/data_manager_sam_fasta_index_builder/2a1ac1abc3f7/data_manager_sam_fasta_index_builder/tool-data/fasta_indexes.loc.sample --- a/samtools/data_manager_sam_fasta_index_builder/2a1ac1abc3f7/data_manager_sam_fasta_index_builder/tool-data/fasta_indexes.loc.sample Fri Oct 04 08:07:15 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,29 +0,0 @@ -#This is a sample file distributed with Galaxy that enables tools -#to use a directory of Samtools indexed sequences data files. You will need -#to create these data files and then create a fasta_indexes.loc file -#similar to this one (store it in this directory) that points to -#the directories in which those files are stored. The fasta_indexes.loc -#file has this format (white space characters are TAB characters): -# -# -# -#So, for example, if you had hg19 Canonical indexed stored in -# -# /depot/data2/galaxy/hg19/sam/, -# -#then the fasta_indexes.loc entry would look like this: -# -#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa -# -#and your /depot/data2/galaxy/hg19/sam/ directory -#would contain hg19canon.fa and hg19canon.fa.fai files. -# -#Your fasta_indexes.loc file should include an entry per line for -#each index set you have stored. The file in the path does actually -#exist, but it should never be directly used. Instead, the name serves -#as a prefix for the index file. For example: -# -#hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa -#hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa -#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa -#hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa diff -r 5f1b354dc002 -r aba80e38756a samtools/data_manager_sam_fasta_index_builder/2a1ac1abc3f7/data_manager_sam_fasta_index_builder/tool_data_table_conf.xml.sample --- a/samtools/data_manager_sam_fasta_index_builder/2a1ac1abc3f7/data_manager_sam_fasta_index_builder/tool_data_table_conf.xml.sample Fri Oct 04 08:07:15 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,12 +0,0 @@ - - - - - value, dbkey, name, path - -
- - value, dbkey, name, path - -
- diff -r 5f1b354dc002 -r aba80e38756a samtools/data_manager_sam_fasta_index_builder/2a1ac1abc3f7/data_manager_sam_fasta_index_builder/tool_dependencies.xml --- a/samtools/data_manager_sam_fasta_index_builder/2a1ac1abc3f7/data_manager_sam_fasta_index_builder/tool_dependencies.xml Fri Oct 04 08:07:15 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ - - - - - - diff -r 5f1b354dc002 -r aba80e38756a samtools/package_cairo_1_12_14/cd2ed5717e38/package_cairo_1_12_14/tool_dependencies.xml --- a/samtools/package_cairo_1_12_14/cd2ed5717e38/package_cairo_1_12_14/tool_dependencies.xml Fri Oct 04 08:07:15 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,58 +0,0 @@ - - - - - - - - - - - - - - - - - - http://depot.galaxyproject.org/package/source/cairo/cairo-1.12.14.tar.bz2 - - - - - - - - - - - - - - - - - sed -i.bak 's|MAYBE_WARN="$MAYBE_WARN -flto"|MAYBE_WARN="$MAYBE_WARN -flto -ffat-lto-objects -fuse-linker-plugin" |' configure build/configure.ac.warnings - - --enable-quartz=no --enable-quartz-font=no --with-x=no --enable-xcb-shm=no --enable-xlib-xcb=no --enable-xcb=no --enable-gtk-doc=no --enable-gtk-doc-html=no --enable-xlib-xrender=no - - touch $INSTALL_DIR/include/cairo/cairo-xlib.h - - $INSTALL_DIR/bin - $INSTALL_DIR/lib - $INSTALL_DIR/lib - $INSTALL_DIR/include - $INSTALL_DIR/include - $INSTALL_DIR/include - $INSTALL_DIR/include/cairo - $INSTALL_DIR/include/cairo - $INSTALL_DIR/lib/pkgconfig - -I$INSTALL_DIR/include/cairo - "-L$INSTALL_DIR/lib -lcairo" - - - - - - - diff -r 5f1b354dc002 -r aba80e38756a samtools/package_freetype_2_5_2/a65217367e4a/package_freetype_2_5_2/tool_dependencies.xml --- a/samtools/package_freetype_2_5_2/a65217367e4a/package_freetype_2_5_2/tool_dependencies.xml Fri Oct 04 08:07:15 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,30 +0,0 @@ - - - - - - - - - http://download.savannah.gnu.org/releases/freetype/freetype-2.5.2.tar.gz - - - - - - - - $INSTALL_DIR/lib - $INSTALL_DIR/bin - $INSTALL_DIR/lib - $INSTALL_DIR/lib - $INSTALL_DIR/include/freetype2 - $INSTALL_DIR/include/freetype2 - $INSTALL_DIR/lib/pkgconfig - - - - - - - diff -r 5f1b354dc002 -r aba80e38756a samtools/package_libpng_1_6_7/3de32cd300a9/package_libpng_1_6_7/tool_dependencies.xml --- a/samtools/package_libpng_1_6_7/3de32cd300a9/package_libpng_1_6_7/tool_dependencies.xml Fri Oct 04 08:07:15 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,20 +0,0 @@ - - - - - - http://downloads.sourceforge.net/project/libpng/libpng16/older-releases/1.6.7/libpng-1.6.7.tar.gz - - - $INSTALL_DIR/bin - $INSTALL_DIR - $INSTALL_DIR/lib - $INSTALL_DIR/include - $INSTALL_DIR/lib - $INSTALL_DIR/lib/pkgconfig - - - - - - diff -r 5f1b354dc002 -r aba80e38756a samtools/package_ncurses_5_9/tool_dependencies.xml --- a/samtools/package_ncurses_5_9/tool_dependencies.xml Fri Oct 04 08:07:15 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,41 +0,0 @@ - - - - - - - http://ftp.gnu.org/pub/gnu/ncurses/ncurses-5.9.tar.gz - https://depot.galaxyproject.org/software/ncurses_patch/ncurses_patch_5.9p_src_all.patch - - patch ncurses/base/MKlib_gen.sh ncurses_patch_5.9p_src_all.patch - - --with-shared --enable-symlinks - - - http://ftp.gnu.org/pub/gnu/ncurses/ncurses-5.9.tar.gz - https://depot.galaxyproject.org/software/ncurses_patch/ncurses_patch_5.9p_src_all.patch - - patch ncurses/base/MKlib_gen.sh ncurses_patch_5.9p_src_all.patch - - --with-shared --enable-symlinks --without-cxx --without-cxx-binding --without-ada --without-progs --without-curses-h --without-debug --enable-widec --enable-const --enable-ext-colors --enable-sigwinch --enable-wgetch-events - - - $INSTALL_DIR/include - $INSTALL_DIR/lib/ - $INSTALL_DIR - $INSTALL_DIR/lib - $INSTALL_DIR/lib - $INSTALL_DIR/lib - $INSTALL_DIR/include - $INSTALL_DIR/include - $INSTALL_DIR/include/ncurses - $INSTALL_DIR/include/ncurses - - - - - ncurses (new curses) is a programming library that provides an API which allows the programmer - to write text-based user interfaces in a terminal-independent manner - - - diff -r 5f1b354dc002 -r aba80e38756a samtools/package_pixman_0_32_4/93cd8e03820c/package_pixman_0_32_4/tool_dependencies.xml --- a/samtools/package_pixman_0_32_4/93cd8e03820c/package_pixman_0_32_4/tool_dependencies.xml Fri Oct 04 08:07:15 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,46 +0,0 @@ - - - - - - - - - - - http://cairographics.org/releases/pixman-0.32.4.tar.gz - - - - - - - - - $INSTALL_DIR/bin - $INSTALL_DIR/lib - $INSTALL_DIR/lib/pkgconfig - - - - - http://cairographics.org/releases/pixman-0.32.4.tar.gz - - - - - - - --disable-mmx - - $INSTALL_DIR/bin - $INSTALL_DIR/lib - $INSTALL_DIR/lib - $INSTALL_DIR/lib/pkgconfig - - - - - - - diff -r 5f1b354dc002 -r aba80e38756a samtools/package_samtools_0_1_19/95d2c4aefb5f/package_samtools_0_1_19/tool_dependencies.xml --- a/samtools/package_samtools_0_1_19/95d2c4aefb5f/package_samtools_0_1_19/tool_dependencies.xml Fri Oct 04 08:07:15 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,79 +0,0 @@ - - - - - - - http://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-0.1.19-Linux-x86_64.tgz - - . - $INSTALL_DIR - - - - http://depot.galaxyproject.org/package/darwin/x86_64/samtools/samtools-0.1.19-Darwin-x86_64.tgz - - . - $INSTALL_DIR - - - - http://depot.galaxyproject.org/package/source/samtools/samtools-0.1.19.tar.bz2 - sed -i.bak 's/-lcurses/-lncurses/' Makefile - make - - samtools - $INSTALL_DIR/bin - - - bcftools/bcftools - $INSTALL_DIR/bin - - - bcftools/vcfutils.pl - $INSTALL_DIR/bin - - - libbam.a - $INSTALL_DIR/lib - - - . - $INSTALL_DIR/include/bam - - - - $INSTALL_DIR/bin - $INSTALL_DIR/lib - $INSTALL_DIR - - - - -Program: samtools (Tools for alignments in the SAM format) -Version: 0.1.19-44428cd - -Usage: samtools <command> [options] - -Command: view SAM<->BAM conversion - sort sort alignment file - mpileup multi-way pileup - depth compute the depth - faidx index/extract FASTA - tview text alignment viewer - index index alignment - idxstats BAM index stats (r595 or later) - fixmate fix mate information - flagstat simple stats - calmd recalculate MD/NM tags and '=' bases - merge merge sorted alignments - rmdup remove PCR duplicates - reheader replace BAM header - cat concatenate BAMs - bedcov read depth per BED region - targetcut cut fosmid regions (for fosmid pool only) - phase phase heterozygotes - bamshuf shuffle and group alignments by name - - - diff -r 5f1b354dc002 -r aba80e38756a samtools/package_samtools_1_2/tool_dependencies.xml --- a/samtools/package_samtools_1_2/tool_dependencies.xml Fri Oct 04 08:07:15 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,81 +0,0 @@ - - - - - - - - - - - - - http://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-1.2-Linux-x86_64.tgz - - . - $INSTALL_DIR - - - - https://github.com/samtools/samtools/releases/download/1.2/samtools-1.2.tar.bz2 - - - - - - - - - sed -i.bak 's#/usr/local#$INSTALL_DIR#' Makefile - sed -i.bak -e 's/-lcurses/-lncurses/' Makefile - sed -i.bak -e "s|CFLAGS=\s*-g\s*-Wall\s*-O2\s*|CFLAGS= -g -Wall -O2 -I$NCURSES_INCLUDE_PATH/ncurses/ -I$NCURSES_INCLUDE_PATH -L$NCURSES_LIB_PATH|g" Makefile - - - samtools - $INSTALL_DIR/bin - - - - $INSTALL_DIR/bin - $INSTALL_DIR - - - - -Program: samtools (Tools for alignments in the SAM format) -Version: 1.2 - -Usage: samtools <command> [options] - -Commands: - -- indexing - faidx index/extract FASTA - index index alignment - -- editing - calmd recalculate MD/NM tags and '=' bases - fixmate fix mate information - reheader replace BAM header - rmdup remove PCR duplicates - targetcut cut fosmid regions (for fosmid pool only) - -- file operations - bamshuf shuffle and group alignments by name - cat concatenate BAMs - merge merge sorted alignments - mpileup multi-way pileup - sort sort alignment file - split splits a file by read group - bam2fq converts a BAM to a FASTQ - -- stats - bedcov read depth per BED region - depth compute the depth - flagstat simple stats - idxstats BAM index stats - phase phase heterozygotes - stats generate stats (former bamcheck) - -- viewing - flags explain BAM flags - tview text alignment viewer - view SAM<->BAM<->CRAM conversion - - - diff -r 5f1b354dc002 -r aba80e38756a samtools/package_zlib_1_2_8/tool_dependencies.xml --- a/samtools/package_zlib_1_2_8/tool_dependencies.xml Fri Oct 04 08:07:15 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,23 +0,0 @@ - - - - - - https://depot.galaxyproject.org/software/zlib/zlib_1.2.8_src_all.tar.gz - - - $INSTALL_DIR - $INSTALL_DIR/lib/pkgconfig - $INSTALL_DIR/lib - $INSTALL_DIR/lib - $INSTALL_DIR/include - $INSTALL_DIR/include - - - - - A Massively Spiffy Yet Delicately Unobtrusive Compression Library. - http://www.zlib.net/ - - - diff -r 5f1b354dc002 -r aba80e38756a samtools/suite_samtools_1_2/5b673ccc8747/suite_samtools_1_2/repository_dependencies.xml --- a/samtools/suite_samtools_1_2/5b673ccc8747/suite_samtools_1_2/repository_dependencies.xml Fri Oct 04 08:07:15 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,17 +0,0 @@ - - - - - - - - - - - - - - - - -