Mercurial > repos > scisjnu123 > test
changeset 36:5f1b354dc002 draft
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--- /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
--- /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()
--- /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 @@ +<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>
--- /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 @@ +<?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>
--- /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): +# +#<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. +#
--- /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): +# +# <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
--- /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 @@ +<!-- 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>
--- /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 @@ +<?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>
--- /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 @@ +<?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>
--- /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 @@ +<?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">$INSTALL_DIR/lib/pkgconfig</environment_variable> + </action> + </actions> + </install> + <readme> + </readme> + </package> +</tool_dependency>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/package_libpng_1_6_7/3de32cd300a9/package_libpng_1_6_7/tool_dependencies.xml Fri Oct 04 08:07:15 2019 -0400 @@ -0,0 +1,20 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="libpng" version="1.6.7"> + <install version="1.0"> + <actions> + <action type="download_by_url">http://downloads.sourceforge.net/project/libpng/libpng16/older-releases/1.6.7/libpng-1.6.7.tar.gz</action> + <action type="autoconf"/> + <action type="set_environment"> + <environment_variable action="prepend_to" name="PATH">$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">$INSTALL_DIR/lib/pkgconfig</environment_variable> + </action> + </actions> + </install> + <readme /> + </package> +</tool_dependency>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/package_ncurses_5_9/tool_dependencies.xml Fri Oct 04 08:07:15 2019 -0400 @@ -0,0 +1,41 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="ncurses" version="5.9"> + <install version="1.0"> + <actions_group> + <actions os="linux" architecture="x86_64"> + <action type="download_by_url" sha256sum="9046298fb440324c9d4135ecea7879ffed8546dd1b58e59430ea07a4633f563b">http://ftp.gnu.org/pub/gnu/ncurses/ncurses-5.9.tar.gz</action> + <action type="download_file" sha256sum="c9033021022979a02621af43883e6ca5a4df14d2c3a5a821e4c67923d13d5e78">https://depot.galaxyproject.org/software/ncurses_patch/ncurses_patch_5.9p_src_all.patch</action> + <action type="shell_command"> + patch ncurses/base/MKlib_gen.sh ncurses_patch_5.9p_src_all.patch + </action> + <action type="autoconf">--with-shared --enable-symlinks</action> + </actions> + <actions os="darwin" architecture="x86_64"> + <action type="download_by_url" sha256sum="9046298fb440324c9d4135ecea7879ffed8546dd1b58e59430ea07a4633f563b">http://ftp.gnu.org/pub/gnu/ncurses/ncurses-5.9.tar.gz</action> + <action type="download_file" sha256sum="c9033021022979a02621af43883e6ca5a4df14d2c3a5a821e4c67923d13d5e78">https://depot.galaxyproject.org/software/ncurses_patch/ncurses_patch_5.9p_src_all.patch</action> + <action type="shell_command"> + patch ncurses/base/MKlib_gen.sh ncurses_patch_5.9p_src_all.patch + </action> + <action type="autoconf">--with-shared --enable-symlinks --without-cxx --without-cxx-binding --without-ada --without-progs --without-curses-h --without-debug --enable-widec --enable-const --enable-ext-colors --enable-sigwinch --enable-wgetch-events</action> + </actions> + <action type="set_environment"> + <environment_variable action="set_to" name="NCURSES_INCLUDE_PATH">$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">$INSTALL_DIR/include/ncurses</environment_variable> + </action> + </actions_group> + </install> + <readme> + ncurses (new curses) is a programming library that provides an API which allows the programmer + to write text-based user interfaces in a terminal-independent manner + </readme> + </package> +</tool_dependency>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools/package_pixman_0_32_4/93cd8e03820c/package_pixman_0_32_4/tool_dependencies.xml Fri Oct 04 08:07:15 2019 -0400 @@ -0,0 +1,46 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="libpng" version="1.6.7"> + <repository changeset_revision="3de32cd300a9" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="pixman" version="0.32.4"> + <install version="1.0"> + <actions_group> + <actions architecture="x86_64" os="linux"> + <action sha256sum="80c7ed420e8a3ae749800241e6347c3d55681296cab71384be7969cd9e657e84" type="download_by_url"> + http://cairographics.org/releases/pixman-0.32.4.tar.gz + </action> + <action type="set_environment_for_install"> + <repository changeset_revision="3de32cd300a9" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"> + <package name="libpng" version="1.6.7" /> + </repository> + </action> + <action type="autoconf" /> + <action type="set_environment"> + <environment_variable action="prepend_to" name="PATH">$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>
--- /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 @@ +<?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>
--- /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 @@ +<?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>
--- /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 @@ +<?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>
--- /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 @@ +<?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>