# HG changeset patch
# User takadonet
# Date 1389887832 18000
# Node ID 75064adad44247a18b0dc981e85e3daba8fa8101
Uploaded
diff -r 000000000000 -r 75064adad442 bgzip.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/bgzip.xml Thu Jan 16 10:57:12 2014 -0500
@@ -0,0 +1,50 @@
+
+ Block compression/decompression utility. Required for use of tabix.
+
+ tabix
+
+
+ bgzip
+
+ #if str($virtualOffset) != ""
+ -b $virtualOffset
+ #end if
+
+ #if str($size) != ""
+ -s $size
+ #end if
+
+ $input
+ -c > $output
+
+
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+
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+
+
+**What it does:**
+
+The input data file is sorted and compressed by bgzip which has a gzip(1) like interface. Tabix requires the file to be compressed using this tool first.
+
+**Citation:**
+
+Tabix was written by Heng Li. The BGZF library was originally implemented by Bob Handsaker and modified by Heng Li for remote file access and in-memory caching.
+
+http://samtools.sourceforge.net/tabix.shtml
+
+**Example:**
+
+(grep ^"#" in.gff; grep -v ^"#" in.gff | sort -k1,1 -k4,4n) | bgzip > sorted.gff.gz;
+
+tabix -p gff sorted.gff.gz;
+
+tabix sorted.gff.gz chr1:10,000,000-20,000,000;
+
+
+
diff -r 000000000000 -r 75064adad442 tabix.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tabix.sh Thu Jan 16 10:57:12 2014 -0500
@@ -0,0 +1,12 @@
+#!/bin/bash
+
+
+output=$1
+shift
+#get working directory so we can find the output files
+CUR_DIR=`pwd`
+
+#run tabix
+$CUR_DIR/tabix.sh $@ > $output
+
+exit 0
diff -r 000000000000 -r 75064adad442 tabix.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tabix.xml Thu Jan 16 10:57:12 2014 -0500
@@ -0,0 +1,89 @@
+
+ Generic indexer for TAB-delimited genome position files.
+
+ tabix
+
+
+ tabix.sh $output
+ #if str($optional.extension) == "tabular"
+ #if str($optional.position) == "no"
+ -0
+ #end if
+
+ #if str($optional.columnseq) != ""
+ -s $optional.columnseq
+ #end if
+
+ #if str($optional.columnstart) != ""
+ -b $optional.columnstart
+ #end if
+
+ #if str($optional.columnend) != ""
+ -e $optional.columnend
+ #end if
+
+ #if str($optional.skiplines) != ""
+ -S $optional.skiplines
+ #end if
+
+ #if str($optional.skipchar) != ""
+ -c $optional.skipchar
+ #end if
+ #else
+ -p
+ #end if
+
+ $input $region
+
+
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+
+
+**What it does:**
+
+Tabix indexes a TAB-delimited genome position file in.tab.bgz and creates an index file in.tab.bgz.tbi when region is absent from the command-line. The input data file must be position sorted and compressed by bgzip which has a gzip(1) like interface. After indexing, tabix is able to quickly retrieve data lines overlapping regions specified in the format "chr:beginPos-endPos". Fast data retrieval also works over network if URI is given as a file name and in this case the index file will be downloaded if it is not present locally.
+
+**Citation:**
+
+Tabix was written by Heng Li. The BGZF library was originally implemented by Bob Handsaker and modified by Heng Li for remote file access and in-memory caching.
+
+http://samtools.sourceforge.net/tabix.shtml
+
+**Example:**
+
+(grep ^"#" in.gff; grep -v ^"#" in.gff | sort -k1,1 -k4,4n) | bgzip > sorted.gff.gz;
+
+tabix -p gff sorted.gff.gz;
+
+tabix sorted.gff.gz chr1:10,000,000-20,000,000;
+
+
+
diff -r 000000000000 -r 75064adad442 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Thu Jan 16 10:57:12 2014 -0500
@@ -0,0 +1,27 @@
+
+
+
+
+
+ http://sourceforge.net/projects/samtools/files/tabix/tabix-0.2.6.tar.bz2
+ make
+
+ tabix
+ $INSTALL_DIR/bin
+
+
+ bgzip
+ $INSTALL_DIR/bin
+
+
+ $INSTALL_DIR/bin
+
+
+
+
+ Tabix version 0.2.6. Tabix was written by Heng Li. The BGZF library was originally implemented by Bob Handsaker and modified by Heng Li for remote file access and in-memory caching.
+
+
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+