# HG changeset patch # User scisjnu123 # Date 1570190835 14400 # Node ID 5f1b354dc002377a42fb0527c110e33028e8c965 # Parent 8aaed121d7cd40abf31c899a10662492021db972 Uploaded diff -r 8aaed121d7cd -r 5f1b354dc002 samtools/data_manager_sam_fasta_index_builder/2a1ac1abc3f7/data_manager_sam_fasta_index_builder/README --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/data_manager_sam_fasta_index_builder/2a1ac1abc3f7/data_manager_sam_fasta_index_builder/README Fri Oct 04 08:07:15 2019 -0400 @@ -0,0 +1,1 @@ +TODO diff -r 8aaed121d7cd -r 5f1b354dc002 samtools/data_manager_sam_fasta_index_builder/2a1ac1abc3f7/data_manager_sam_fasta_index_builder/data_manager/data_manager_sam_fasta_index_builder.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/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 @@ -0,0 +1,87 @@ +#!/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 8aaed121d7cd -r 5f1b354dc002 samtools/data_manager_sam_fasta_index_builder/2a1ac1abc3f7/data_manager_sam_fasta_index_builder/data_manager/data_manager_sam_fasta_index_builder.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/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 @@ -0,0 +1,25 @@ + + 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 8aaed121d7cd -r 5f1b354dc002 samtools/data_manager_sam_fasta_index_builder/2a1ac1abc3f7/data_manager_sam_fasta_index_builder/data_manager_conf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/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 @@ -0,0 +1,22 @@ + + + + + + + + + + + + + ${dbkey}/sam_indexes/${value} + + ${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/sam_indexes/${value}/${path} + abspath + + + + + + diff -r 8aaed121d7cd -r 5f1b354dc002 samtools/data_manager_sam_fasta_index_builder/2a1ac1abc3f7/data_manager_sam_fasta_index_builder/tool-data/all_fasta.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/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 @@ -0,0 +1,18 @@ +#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 8aaed121d7cd -r 5f1b354dc002 samtools/data_manager_sam_fasta_index_builder/2a1ac1abc3f7/data_manager_sam_fasta_index_builder/tool-data/fasta_indexes.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/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 @@ -0,0 +1,29 @@ +#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 8aaed121d7cd -r 5f1b354dc002 samtools/data_manager_sam_fasta_index_builder/2a1ac1abc3f7/data_manager_sam_fasta_index_builder/tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/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 @@ -0,0 +1,12 @@ + + + + + value, dbkey, name, path + +
+ + value, dbkey, name, path + +
+ diff -r 8aaed121d7cd -r 5f1b354dc002 samtools/data_manager_sam_fasta_index_builder/2a1ac1abc3f7/data_manager_sam_fasta_index_builder/tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/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 @@ -0,0 +1,6 @@ + + + + + + diff -r 8aaed121d7cd -r 5f1b354dc002 samtools/package_cairo_1_12_14/cd2ed5717e38/package_cairo_1_12_14/tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/package_cairo_1_12_14/cd2ed5717e38/package_cairo_1_12_14/tool_dependencies.xml Fri Oct 04 08:07:15 2019 -0400 @@ -0,0 +1,58 @@ + + + + + + + + + + + + + + + + + + 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 8aaed121d7cd -r 5f1b354dc002 samtools/package_freetype_2_5_2/a65217367e4a/package_freetype_2_5_2/tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/package_freetype_2_5_2/a65217367e4a/package_freetype_2_5_2/tool_dependencies.xml Fri Oct 04 08:07:15 2019 -0400 @@ -0,0 +1,30 @@ + + + + + + + + + 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 8aaed121d7cd -r 5f1b354dc002 samtools/package_libpng_1_6_7/3de32cd300a9/package_libpng_1_6_7/tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/package_libpng_1_6_7/3de32cd300a9/package_libpng_1_6_7/tool_dependencies.xml Fri Oct 04 08:07:15 2019 -0400 @@ -0,0 +1,20 @@ + + + + + + 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 8aaed121d7cd -r 5f1b354dc002 samtools/package_ncurses_5_9/tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/package_ncurses_5_9/tool_dependencies.xml Fri Oct 04 08:07:15 2019 -0400 @@ -0,0 +1,41 @@ + + + + + + + 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 8aaed121d7cd -r 5f1b354dc002 samtools/package_pixman_0_32_4/93cd8e03820c/package_pixman_0_32_4/tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/package_pixman_0_32_4/93cd8e03820c/package_pixman_0_32_4/tool_dependencies.xml Fri Oct 04 08:07:15 2019 -0400 @@ -0,0 +1,46 @@ + + + + + + + + + + + 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 8aaed121d7cd -r 5f1b354dc002 samtools/package_samtools_0_1_19/95d2c4aefb5f/package_samtools_0_1_19/tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/package_samtools_0_1_19/95d2c4aefb5f/package_samtools_0_1_19/tool_dependencies.xml Fri Oct 04 08:07:15 2019 -0400 @@ -0,0 +1,79 @@ + + + + + + + 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 8aaed121d7cd -r 5f1b354dc002 samtools/package_samtools_1_2/tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/package_samtools_1_2/tool_dependencies.xml Fri Oct 04 08:07:15 2019 -0400 @@ -0,0 +1,81 @@ + + + + + + + + + + + + + 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 8aaed121d7cd -r 5f1b354dc002 samtools/package_zlib_1_2_8/tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/package_zlib_1_2_8/tool_dependencies.xml Fri Oct 04 08:07:15 2019 -0400 @@ -0,0 +1,23 @@ + + + + + + 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 8aaed121d7cd -r 5f1b354dc002 samtools/suite_samtools_1_2/5b673ccc8747/suite_samtools_1_2/repository_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/suite_samtools_1_2/5b673ccc8747/suite_samtools_1_2/repository_dependencies.xml Fri Oct 04 08:07:15 2019 -0400 @@ -0,0 +1,17 @@ + + + + + + + + + + + + + + + + +