Mercurial > repos > yhoogstrate > varscan_mpileup2snp_from_bam
changeset 41:b4185ce77360
Uploaded
| author | yhoogstrate |
|---|---|
| date | Wed, 05 Mar 2014 07:15:04 -0500 |
| parents | ff87ad6669eb |
| children | bf9c5a61b200 |
| files | tool-data/all_fasta.loc.sample tool_data_table_conf.xml.sample tool_dependencies.xml |
| diffstat | 3 files changed, 0 insertions(+), 146 deletions(-) [+] |
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--- a/tool-data/all_fasta.loc.sample Wed Mar 05 05:44:50 2014 -0500 +++ /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/tool_data_table_conf.xml.sample Wed Mar 05 05:44:50 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,8 +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> -</tables> \ No newline at end of file
--- a/tool_dependencies.xml Wed Mar 05 05:44:50 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,120 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <!-- Optimized samtools (for threaded mpileup) --> - <package name="samtools-parallel-mpileup" version="0.1.19"> - <install version="1.0"> - <actions> - <action type="shell_command">svn checkout https://github.com/yhoogstrate/parallel-mpileup/trunk samtools-parallel-mpileup && cd samtools-parallel-mpileup && cd $(ls |grep samtools-) && make && cp samtools ../samtools-parallel-mpileup</action> - <action type="move_file"> - <source>samtools-parallel-mpileup</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> - <environment_variable name="PATH" action="prepend_to">$REPOSITORY_INSTALL_DIR</environment_variable> - </action> - </actions> - </install> - <readme> - Downloads and installs a modified version of samtools, able to paralellize the mpileup function. - </readme> - </package> - - <!-- Classical samtools (doesn't support threaded mpileup) --> - <package name="samtools" version="0.1.19"> - <install version="1.0"> - <actions> - <action type="download_by_url">http://downloads.sourceforge.net/project/samtools/samtools/0.1.19/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="shell_command">chmod ugo+rx misc/*.p?</action> - <action type="shell_command">mkdir misc/bin</action> - <action type="shell_command">cp -p `find misc -type f -perm -555` misc/bin/</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>$INSTALL_DIR/bin</destination> - </action> - <action type="move_directory_files"> - <source_directory>misc/bin</source_directory> - <destination_directory>$INSTALL_DIR/bin</destination_directory> - </action> - <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> - </action> - </actions> - </install> - <readme> -Program: samtools (Tools for alignments in the SAM format) -Version: 0.1.19 - -Usage: samtools <command> [options] - -Command: view SAM<->BAM conversion - sort sort alignment file - mpileup multi-way pileup - depth compute the depth - faidx index/extract FASTA - tview text alignment viewer - index index alignment - idxstats BAM index stats (r595 or later) - fixmate fix mate information - flagstat simple stats - calmd recalculate MD/NM tags and '=' bases - merge merge sorted alignments - rmdup remove PCR duplicates - reheader replace BAM header - cat concatenate BAMs - targetcut cut fosmid regions (for fosmid pool only) - phase phase heterozygotes - -This also installs bcftools and misc utility commands: - bcftools - vcfutils.pl - ace2sam - bamcheck - blast2sam.pl - bowtie2sam.pl - export2sam.pl - interpolate_sam.pl - maq2sam-long - maq2sam-short - md5fa - md5sum-lite - novo2sam.pl - psl2sam.pl - sam2vcf.pl - samtools.pl - soap2sam.pl - varfilter.py - wgsim - wgsim_eval.pl - zoom2sam.pl - </readme> - </package> - - <package name="VarScan" version="2.3.6"> - <install version="1.0"> - <actions> - <action type="download_by_url">http://downloads.sourceforge.net/project/varscan/VarScan.v2.3.6.jar</action> - <action type="move_file"> - <source>VarScan.v2.3.6.jar</source> - <destination>$INSTALL_DIR/jars</destination> - </action> - <action type="set_environment"> - <environment_variable name="JAVA_JAR_PATH" action="set_to">$INSTALL_DIR/jars</environment_variable> - </action> - </actions> - </install> - <readme> - Downloads VarScan2. - </readme> - </package> -</tool_dependency> \ No newline at end of file