Mercurial > repos > scisjnu123 > test
changeset 37:aba80e38756a draft
Deleted selected files
| author | scisjnu123 |
|---|---|
| date | Fri, 04 Oct 2019 08:29:04 -0400 |
| parents | 5f1b354dc002 |
| children | 4ea7e783c5ac |
| files | samtools/data_manager_sam_fasta_index_builder/2a1ac1abc3f7/data_manager_sam_fasta_index_builder/README samtools/data_manager_sam_fasta_index_builder/2a1ac1abc3f7/data_manager_sam_fasta_index_builder/data_manager/data_manager_sam_fasta_index_builder.py samtools/data_manager_sam_fasta_index_builder/2a1ac1abc3f7/data_manager_sam_fasta_index_builder/data_manager/data_manager_sam_fasta_index_builder.xml samtools/data_manager_sam_fasta_index_builder/2a1ac1abc3f7/data_manager_sam_fasta_index_builder/data_manager_conf.xml samtools/data_manager_sam_fasta_index_builder/2a1ac1abc3f7/data_manager_sam_fasta_index_builder/tool-data/all_fasta.loc.sample samtools/data_manager_sam_fasta_index_builder/2a1ac1abc3f7/data_manager_sam_fasta_index_builder/tool-data/fasta_indexes.loc.sample samtools/data_manager_sam_fasta_index_builder/2a1ac1abc3f7/data_manager_sam_fasta_index_builder/tool_data_table_conf.xml.sample samtools/data_manager_sam_fasta_index_builder/2a1ac1abc3f7/data_manager_sam_fasta_index_builder/tool_dependencies.xml samtools/package_cairo_1_12_14/cd2ed5717e38/package_cairo_1_12_14/tool_dependencies.xml samtools/package_freetype_2_5_2/a65217367e4a/package_freetype_2_5_2/tool_dependencies.xml samtools/package_libpng_1_6_7/3de32cd300a9/package_libpng_1_6_7/tool_dependencies.xml samtools/package_ncurses_5_9/tool_dependencies.xml samtools/package_pixman_0_32_4/93cd8e03820c/package_pixman_0_32_4/tool_dependencies.xml samtools/package_samtools_0_1_19/95d2c4aefb5f/package_samtools_0_1_19/tool_dependencies.xml samtools/package_samtools_1_2/tool_dependencies.xml samtools/package_zlib_1_2_8/tool_dependencies.xml samtools/suite_samtools_1_2/5b673ccc8747/suite_samtools_1_2/repository_dependencies.xml |
| diffstat | 17 files changed, 0 insertions(+), 595 deletions(-) [+] |
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--- 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
--- 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()
--- 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 @@ -<tool id="sam_fasta_index_builder" name="SAM FASTA index" tool_type="manage_data" version="0.0.2"> - <description>builder</description> - <requirements> - <requirement type="package" version="0.1.19">samtools</requirement> - </requirements> - <command interpreter="python">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"</command> - <inputs> - <param name="all_fasta_source" type="select" label="Source FASTA Sequence"> - <options from_data_table="all_fasta"/> - </param> - <param type="text" name="sequence_name" value="" label="Name of sequence" /> - <param type="text" name="sequence_id" value="" label="ID for sequence" /> - </inputs> - <outputs> - <data name="out_file" format="data_manager_json"/> - </outputs> - - <help> - -.. class:: infomark - -**Notice:** If you leave name, description, or id blank, it will be generated automatically. - - </help> -</tool>
--- 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 @@ -<?xml version="1.0"?> -<data_managers> - - <data_manager tool_file="data_manager/data_manager_sam_fasta_index_builder.xml" id="sam_fasta_index_builder" version="0.0.1"> - <data_table name="fasta_indexes"> - <output> - <column name="value" /> - <column name="dbkey" /> - <column name="name" /> - <column name="path" output_ref="out_file" > - <move type="directory" relativize_symlinks="True"> - <!-- <source>${path}</source>--> <!-- out_file.extra_files_path is used as base by default --> <!-- if no source, eg for type=directory, then refers to base --> - <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${dbkey}/sam_indexes/${value}</target> - </move> - <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/sam_indexes/${value}/${path}</value_translation> - <value_translation type="function">abspath</value_translation> - </column> - </output> - </data_table> - </data_manager> - -</data_managers>
--- 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): -# -#<unique_build_id> <dbkey> <display_name> <file_path> -# -#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. -#
--- 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): -# -# <unique_build_id> <dbkey> <display_name> <file_base_path> -# -#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
--- 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 @@ -<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> -<tables> - <!-- Locations of all fasta files under genome directory --> - <table name="all_fasta" comment_char="#"> - <columns>value, dbkey, name, path</columns> - <file path="tool-data/all_fasta.loc" /> - </table> - <table name="fasta_indexes" comment_char="#"> - <columns>value, dbkey, name, path</columns> - <file path="tool-data/fasta_indexes.loc" /> - </table> -</tables>
--- 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 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="samtools" version="0.1.19"> - <repository changeset_revision="95d2c4aefb5f" name="package_samtools_0_1_19" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency>
--- 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 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="pixman" version="0.32.4"> - <repository changeset_revision="93cd8e03820c" name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="libpng" version="1.6.7"> - <repository changeset_revision="3de32cd300a9" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="freetype" version="2.5.2"> - <repository changeset_revision="a65217367e4a" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="fontconfig" version="2.11.1"> - <repository changeset_revision="2ce32675340e" name="package_fontconfig_2_11_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="cairo" version="1.12.14"> - <install version="1.0"> - <actions> - <action type="download_by_url">http://depot.galaxyproject.org/package/source/cairo/cairo-1.12.14.tar.bz2</action> - <action type="set_environment_for_install"> - <repository changeset_revision="93cd8e03820c" name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"> - <package name="pixman" version="0.32.4" /> - </repository> - <repository changeset_revision="3de32cd300a9" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"> - <package name="libpng" version="1.6.7" /> - </repository> - <repository changeset_revision="a65217367e4a" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"> - <package name="freetype" version="2.5.2" /> - </repository> - <repository changeset_revision="2ce32675340e" name="package_fontconfig_2_11_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"> - <package name="fontconfig" version="2.11.1" /> - </repository> - </action> - <!-- edit configure and build/configure.ac.warnings to allow compiling cairo on gcc-4.9. Fixed in more recent versions of cairo --> - <action type="shell_command"> - 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 - </action> - <action type="autoconf">--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</action> - <!-- Create an empty cairo-xlib.h file, because R's configure script explicitly includes it even if X is disabled. --> - <action type="shell_command">touch $INSTALL_DIR/include/cairo/cairo-xlib.h</action> - <action type="set_environment"> - <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> - <environment_variable action="prepend_to" name="CAIRO_LIB_PATH">$INSTALL_DIR/lib</environment_variable> - <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib</environment_variable> - <environment_variable action="prepend_to" name="CAIRO_INCLUDE_PATH">$INSTALL_DIR/include</environment_variable> - <environment_variable action="prepend_to" name="C_INCLUDE_PATH">$INSTALL_DIR/include</environment_variable> - <environment_variable action="prepend_to" name="CPLUS_INCLUDE_PATH">$INSTALL_DIR/include</environment_variable> - <environment_variable action="prepend_to" name="C_INCLUDE_PATH">$INSTALL_DIR/include/cairo</environment_variable> - <environment_variable action="prepend_to" name="CPLUS_INCLUDE_PATH">$INSTALL_DIR/include/cairo</environment_variable> - <environment_variable action="prepend_to" name="PKG_CONFIG_PATH">$INSTALL_DIR/lib/pkgconfig</environment_variable> - <environment_variable action="set_to" name="CAIRO_CFLAGS">-I$INSTALL_DIR/include/cairo</environment_variable> - <environment_variable action="set_to" name="CAIRO_LIBS">"-L$INSTALL_DIR/lib -lcairo"</environment_variable> - </action> - </actions> - </install> - <readme> - </readme> - </package> -</tool_dependency>
--- 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 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="libpng" version="1.6.7"> - <repository changeset_revision="f48b920cae1f" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="freetype" version="2.5.2"> - <install version="1.0"> - <actions> - <action type="download_by_url">http://download.savannah.gnu.org/releases/freetype/freetype-2.5.2.tar.gz</action> - <action type="set_environment_for_install"> - <repository changeset_revision="f48b920cae1f" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"> - <package name="libpng" version="1.6.7" /> - </repository> - </action> - <action type="autoconf" /> - <action type="set_environment"> - <environment_variable action="set_to" name="FREETYPE_LIB_PATH">$INSTALL_DIR/lib</environment_variable> - <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> - <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib</environment_variable> - <environment_variable action="prepend_to" name="DYLD_LIBRARY_PATH">$INSTALL_DIR/lib</environment_variable> - <environment_variable action="prepend_to" name="C_INCLUDE_PATH">$INSTALL_DIR/include/freetype2</environment_variable> - <environment_variable action="prepend_to" name="CPLUS_INCLUDE_PATH">$INSTALL_DIR/include/freetype2</environment_variable> - <environment_variable action="prepend_to" name="PKG_CONFIG_PATH">$INSTALL_DIR/lib/pkgconfig</environment_variable> - </action> - </actions> - </install> - <readme> - </readme> - </package> -</tool_dependency>
--- a/samtools/package_libpng_1_6_7/3de32cd300a9/package_libpng_1_6_7/tool_dependencies.xml Fri Oct 04 08:07:15 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,20 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="libpng" version="1.6.7"> - <install version="1.0"> - <actions> - <action type="download_by_url">http://downloads.sourceforge.net/project/libpng/libpng16/older-releases/1.6.7/libpng-1.6.7.tar.gz</action> - <action type="autoconf"/> - <action type="set_environment"> - <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> - <environment_variable action="set_to" name="LIBPNG_ROOT">$INSTALL_DIR</environment_variable> - <environment_variable action="set_to" name="LIBPNG_LIB_PATH">$INSTALL_DIR/lib</environment_variable> - <environment_variable action="set_to" name="LIBPNG_INCLUDE_PATH">$INSTALL_DIR/include</environment_variable> - <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib</environment_variable> - <environment_variable action="prepend_to" name="PKG_CONFIG_PATH">$INSTALL_DIR/lib/pkgconfig</environment_variable> - </action> - </actions> - </install> - <readme /> - </package> -</tool_dependency>
--- a/samtools/package_ncurses_5_9/tool_dependencies.xml Fri Oct 04 08:07:15 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,41 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="ncurses" version="5.9"> - <install version="1.0"> - <actions_group> - <actions os="linux" architecture="x86_64"> - <action type="download_by_url" sha256sum="9046298fb440324c9d4135ecea7879ffed8546dd1b58e59430ea07a4633f563b">http://ftp.gnu.org/pub/gnu/ncurses/ncurses-5.9.tar.gz</action> - <action type="download_file" sha256sum="c9033021022979a02621af43883e6ca5a4df14d2c3a5a821e4c67923d13d5e78">https://depot.galaxyproject.org/software/ncurses_patch/ncurses_patch_5.9p_src_all.patch</action> - <action type="shell_command"> - patch ncurses/base/MKlib_gen.sh ncurses_patch_5.9p_src_all.patch - </action> - <action type="autoconf">--with-shared --enable-symlinks</action> - </actions> - <actions os="darwin" architecture="x86_64"> - <action type="download_by_url" sha256sum="9046298fb440324c9d4135ecea7879ffed8546dd1b58e59430ea07a4633f563b">http://ftp.gnu.org/pub/gnu/ncurses/ncurses-5.9.tar.gz</action> - <action type="download_file" sha256sum="c9033021022979a02621af43883e6ca5a4df14d2c3a5a821e4c67923d13d5e78">https://depot.galaxyproject.org/software/ncurses_patch/ncurses_patch_5.9p_src_all.patch</action> - <action type="shell_command"> - patch ncurses/base/MKlib_gen.sh ncurses_patch_5.9p_src_all.patch - </action> - <action type="autoconf">--with-shared --enable-symlinks --without-cxx --without-cxx-binding --without-ada --without-progs --without-curses-h --without-debug --enable-widec --enable-const --enable-ext-colors --enable-sigwinch --enable-wgetch-events</action> - </actions> - <action type="set_environment"> - <environment_variable action="set_to" name="NCURSES_INCLUDE_PATH">$INSTALL_DIR/include</environment_variable> - <environment_variable action="set_to" name="NCURSES_LIB_PATH">$INSTALL_DIR/lib/</environment_variable> - <environment_variable action="set_to" name="NCURSES_ROOT_PATH">$INSTALL_DIR</environment_variable> - <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib</environment_variable> - <environment_variable action="prepend_to" name="DYLD_LIBRARY_PATH">$INSTALL_DIR/lib</environment_variable> - <environment_variable action="prepend_to" name="LIBRARY_PATH">$INSTALL_DIR/lib</environment_variable> - <environment_variable name="C_INCLUDE_PATH" action="prepend_to">$INSTALL_DIR/include</environment_variable> - <environment_variable name="CPLUS_INCLUDE_PATH" action="prepend_to">$INSTALL_DIR/include</environment_variable> - <environment_variable name="C_INCLUDE_PATH" action="prepend_to">$INSTALL_DIR/include/ncurses</environment_variable> - <environment_variable name="CPLUS_INCLUDE_PATH" action="prepend_to">$INSTALL_DIR/include/ncurses</environment_variable> - </action> - </actions_group> - </install> - <readme> - ncurses (new curses) is a programming library that provides an API which allows the programmer - to write text-based user interfaces in a terminal-independent manner - </readme> - </package> -</tool_dependency>
--- a/samtools/package_pixman_0_32_4/93cd8e03820c/package_pixman_0_32_4/tool_dependencies.xml Fri Oct 04 08:07:15 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,46 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="libpng" version="1.6.7"> - <repository changeset_revision="3de32cd300a9" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="pixman" version="0.32.4"> - <install version="1.0"> - <actions_group> - <actions architecture="x86_64" os="linux"> - <action sha256sum="80c7ed420e8a3ae749800241e6347c3d55681296cab71384be7969cd9e657e84" type="download_by_url"> - http://cairographics.org/releases/pixman-0.32.4.tar.gz - </action> - <action type="set_environment_for_install"> - <repository changeset_revision="3de32cd300a9" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"> - <package name="libpng" version="1.6.7" /> - </repository> - </action> - <action type="autoconf" /> - <action type="set_environment"> - <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> - <environment_variable action="set_to" name="PIXMAN_LIB_PATH">$INSTALL_DIR/lib</environment_variable> - <environment_variable action="prepend_to" name="PKG_CONFIG_PATH">$INSTALL_DIR/lib/pkgconfig</environment_variable> - </action> - </actions> - <actions architecture="x86_64" os="darwin"> - <action sha256sum="80c7ed420e8a3ae749800241e6347c3d55681296cab71384be7969cd9e657e84" type="download_by_url"> - http://cairographics.org/releases/pixman-0.32.4.tar.gz - </action> - <action type="set_environment_for_install"> - <repository changeset_revision="3de32cd300a9" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"> - <package name="libpng" version="1.6.7" /> - </repository> - </action> - <action type="autoconf">--disable-mmx</action> - <action type="set_environment"> - <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> - <environment_variable action="set_to" name="PIXMAN_LIB_PATH">$INSTALL_DIR/lib</environment_variable> - <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib</environment_variable> - <environment_variable action="prepend_to" name="PKG_CONFIG_PATH">$INSTALL_DIR/lib/pkgconfig</environment_variable> - </action> - </actions> - </actions_group> - </install> - <readme /> - </package> -</tool_dependency>
--- 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 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="samtools" version="0.1.19"> - <install version="1.0"> - <actions_group> - <actions os="linux" architecture="x86_64"> - <action type="download_by_url" target_filename="samtools-0.1.19.tgz">http://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-0.1.19-Linux-x86_64.tgz</action> - <action type="move_directory_files"> - <source_directory>.</source_directory> - <destination_directory>$INSTALL_DIR</destination_directory> - </action> - </actions> - <actions os="darwin" architecture="x86_64"> - <action type="download_by_url" target_filename="samtools-0.1.19.tgz">http://depot.galaxyproject.org/package/darwin/x86_64/samtools/samtools-0.1.19-Darwin-x86_64.tgz</action> - <action type="move_directory_files"> - <source_directory>.</source_directory> - <destination_directory>$INSTALL_DIR</destination_directory> - </action> - </actions> - <actions> - <action type="download_by_url">http://depot.galaxyproject.org/package/source/samtools/samtools-0.1.19.tar.bz2</action> - <action type="shell_command">sed -i.bak 's/-lcurses/-lncurses/' Makefile</action> - <action type="shell_command">make</action> - <action type="move_file"> - <source>samtools</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="move_file"> - <source>bcftools/bcftools</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="move_file"> - <source>bcftools/vcfutils.pl</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="move_file"> - <source>libbam.a</source> - <destination>$INSTALL_DIR/lib</destination> - </action> - <action type="move_directory_files"> - <source_directory>.</source_directory> - <destination_directory>$INSTALL_DIR/include/bam</destination_directory> - </action> - </actions> - <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> - <environment_variable name="BAM_LIB_PATH" action="set_to">$INSTALL_DIR/lib</environment_variable> - <environment_variable name="BAM_ROOT" action="set_to">$INSTALL_DIR</environment_variable> - </action> - </actions_group> - </install> - <readme> -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 - </readme> - </package> -</tool_dependency>
--- 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 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="ncurses" version="5.9"> - <repository changeset_revision="5e1760c773ba" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="zlib" version="1.2.8"> - <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="samtools" version="1.2"> - <install version="1.0"> - <actions_group> - <actions architecture="x86_64" os="linux"> - <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-1.2-Linux-x86_64.tgz</action> - <action type="move_directory_files"> - <source_directory>.</source_directory> - <destination_directory>$INSTALL_DIR</destination_directory> - </action> - </actions> - <actions> - <action type="download_by_url">https://github.com/samtools/samtools/releases/download/1.2/samtools-1.2.tar.bz2</action> - <action type="set_environment_for_install"> - <repository changeset_revision="5e1760c773ba" name="package_ncurses_5_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> - <package name="ncurses" version="5.9" /> - </repository> - <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> - <package name="zlib" version="1.2.8" /> - </repository> - </action> - <action type="shell_command">sed -i.bak 's#/usr/local#$INSTALL_DIR#' Makefile</action> - <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/' Makefile</action> - <action type="shell_command">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$NCURSES_LIB_PATH|g" Makefile</action> - <action type="make_install" /> - <action type="move_file"> - <source>samtools</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - </actions> - <action type="set_environment"> - <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> - <environment_variable action="set_to" name="SAMTOOLS_ROOT_PATH">$INSTALL_DIR</environment_variable> - </action> - </actions_group> - </install> - <readme> -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 - </readme> - </package> -</tool_dependency>
--- 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 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="zlib" version="1.2.8"> - <install version="1.0"> - <actions> - <action type="download_by_url" sha256sum="36658cb768a54c1d4dec43c3116c27ed893e88b02ecfcb44f2166f9c0b7f2a0d">https://depot.galaxyproject.org/software/zlib/zlib_1.2.8_src_all.tar.gz</action> - <action type="autoconf" /> - <action type="set_environment"> - <environment_variable name="ZLIB_ROOT_PATH" action="set_to">$INSTALL_DIR</environment_variable> - <environment_variable name="PKG_CONFIG_PATH" action="prepend_to">$INSTALL_DIR/lib/pkgconfig</environment_variable> - <environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$INSTALL_DIR/lib</environment_variable> - <environment_variable name="LIBRARY_PATH" action="prepend_to">$INSTALL_DIR/lib</environment_variable> - <environment_variable name="C_INCLUDE_PATH" action="prepend_to">$INSTALL_DIR/include</environment_variable> - <environment_variable name="CPLUS_INCLUDE_PATH" action="prepend_to">$INSTALL_DIR/include</environment_variable> - </action> - </actions> - </install> - <readme> - A Massively Spiffy Yet Delicately Unobtrusive Compression Library. - http://www.zlib.net/ - </readme> - </package> -</tool_dependency>
--- 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 @@ -<?xml version="1.0"?> -<repositories description="A suite of Galaxy tools designed to work with version 1.2 of the SAMtools package."> - <repository changeset_revision="cf875cbe2df4" name="data_manager_sam_fasta_index_builder" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> - <repository changeset_revision="af7c50162f0b" name="bam_to_sam" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> - <repository changeset_revision="d04d9f1c6791" name="sam_to_bam" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> - <repository changeset_revision="8c3472790020" name="samtools_bedcov" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> - <repository changeset_revision="1ebb4ecdc1ef" name="samtools_calmd" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> - <repository changeset_revision="0072bf593791" name="samtools_flagstat" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> - <repository changeset_revision="87398ae795c7" name="samtools_idxstats" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> - <repository changeset_revision="c6fdfe3331d6" name="samtools_mpileup" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> - <repository changeset_revision="020e144b5f78" name="samtools_reheader" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> - <repository changeset_revision="3735f950b2f5" name="samtools_rmdup" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> - <repository changeset_revision="2b474ebbfc7d" name="samtools_slice_bam" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> - <repository changeset_revision="a430da4f04cd" name="samtools_sort" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> - <repository changeset_revision="57f3e32f809d" name="samtools_split" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> - <repository changeset_revision="0d71d9467847" name="samtools_stats" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> -</repositories>