# HG changeset patch
# User scisjnu123
# Date 1570119458 14400
# Node ID 9eee08ea613b4d54cb5c0b7f57a607c9e84287bb
# Parent 060c2129612fc6f8789830fa96c31d8b5d669f6a
Uploaded
diff -r 060c2129612f -r 9eee08ea613b 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 Thu Oct 03 12:17:38 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 060c2129612f -r 9eee08ea613b 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 Thu Oct 03 12:17:38 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 060c2129612f -r 9eee08ea613b 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 Thu Oct 03 12:17:38 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 060c2129612f -r 9eee08ea613b samtools/samtools-sort/macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/samtools/samtools-sort/macros.xml Thu Oct 03 12:17:38 2019 -0400
@@ -0,0 +1,172 @@
+
+
+
+ samtools
+
+
+
+ 1.9
+ #set $flags = sum(map(int, str($filter).split(',')))
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ ^[^\s'\":]+(:\d+(-\d+){0,1}){0,1}$
+
+
+
+
+
+
+
+
+
+
+
+
+ @misc{SAM_def,
+ title={Definition of SAM/BAM format},
+ url = {https://samtools.github.io/hts-specs/},}
+
+ 10.1093/bioinformatics/btp352
+ 10.1093/bioinformatics/btr076
+ 10.1093/bioinformatics/btr509
+
+ @misc{Danecek_et_al,
+ Author={Danecek, P., Schiffels, S., Durbin, R.},
+ title={Multiallelic calling model in bcftools (-m)},
+ url = {http://samtools.github.io/bcftools/call-m.pdf},}
+
+
+ @misc{Durbin_VCQC,
+ Author={Durbin, R.},
+ title={Segregation based metric for variant call QC},
+ url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},}
+
+
+ @misc{Li_SamMath,
+ Author={Li, H.},
+ title={Mathematical Notes on SAMtools Algorithms},
+ url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},}
+
+
+ @misc{SamTools_github,
+ title={SAMTools GitHub page},
+ url = {https://github.com/samtools/samtools},}
+
+
+
+
+ &1 | grep Version]]>
+
+
+
+
+
+
+
diff -r 060c2129612f -r 9eee08ea613b samtools/samtools-sort/samtools_sort.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/samtools/samtools-sort/samtools_sort.xml Thu Oct 03 12:17:38 2019 -0400
@@ -0,0 +1,169 @@
+
+ order of storing aligned sequences
+
+ macros.xml
+
+
+
+
+ '${output1}'
+ ]]>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+**What it does**
+
+Sort alignments by leftmost coordinates, or by read name when -n is used.
+An appropriate @HD-SO sort order header tag will be added or an existing
+one updated if necessary.
+
+**Ordering Rules**
+
+The following rules are used for ordering records.
+
+If option -t is in use, records are first sorted by the value of the given
+alignment tag, and then by position or name (if using -n). For example, “-t RG”
+will make read group the primary sort key. The rules for ordering by tag are:
+
+- Records that do not have the tag are sorted before ones that do.
+- If the types of the tags are different, they will be sorted so that single
+ character tags (type A) come before array tags (type B), then string tags
+ (types H and Z), then numeric tags (types f and i).
+- Numeric tags (types f and i) are compared by value. Note that comparisons of
+ floating-point values are subject to issues of rounding and precision.
+- String tags (types H and Z) are compared based on the binary contents of the
+ tag using the C strcmp(3) function.
+- Character tags (type A) are compared by binary character value.
+- No attempt is made to compare tags of other types — notably type B array values will not be compared.
+
+When the -n option is present, records are sorted by name. Names are compared so as to give a “natural” ordering — i.e. sections consisting of digits are compared numerically while all other sections are compared based on their binary representation. This means “a1” will come before “b1” and “a9” will come before “a10”. Records with the same name will be ordered according to the values of the READ1 and READ2 flags (see flags).
+
+When the -n option is not present, reads are sorted by reference (according to the order of the @SQ header records), then by position in the reference, and then by the REVERSE flag.
+
+This has now been removed. The previous out.prefix argument (and -f option, if any) should be changed to an appropriate combination of -T PREFIX and -o FILE. The previous -o option should be removed, as output defaults to standard output.
+
+
+
+
diff -r 060c2129612f -r 9eee08ea613b samtools/samtools_sort/macros.xml
--- a/samtools/samtools_sort/macros.xml Thu Oct 03 11:27:47 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,70 +0,0 @@
-
-
-
- samtools
-
-
-
-
-
-
- @misc{SAM_def,
- title={Definition of SAM/BAM format},
- url = {https://samtools.github.io/hts-specs/SAMv1.pdf},}
-
- 10.1093/bioinformatics/btp352
- 10.1093/bioinformatics/btr076
- 10.1093/bioinformatics/btr509
-
- @misc{Danecek_et_al,
- Author={Danecek, P., Schiffels, S., Durbin, R.},
- title={Multiallelic calling model in bcftools (-m)},
- url = {http://samtools.github.io/bcftools/call-m.pdf},}
-
-
- @misc{Durbin_VCQC,
- Author={Durbin, R.},
- title={Segregation based metric for variant call QC},
- url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},}
-
-
- @misc{Li_SamMath,
- Author={Li, H.},
- title={Mathematical Notes on SAMtools Algorithms},
- url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},}
-
-
- @misc{SamTools_github,
- title={SAMTools GitHub page},
- url = {https://github.com/samtools/samtools},}
-
-
-
-
- samtools --version | head -n 1 | awk '{ print $2 }'
-
-
-
-
-
-
-
------
-
-.. class:: warningmark
-
-**No options available? How to re-detect metadata**
-
-If you see a "No options available" within the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop down, you need to re-detect metadata for the dataset you are trying to process. To do this follow these steps:
-
-1. Click on the **pencil** icon adjacent to the dataset in the history
-2. A new menu will appear in the center pane of the interface
-3. Click **Datatype** tab
-4. Set **New Type** to **BAM**
-5. Click **Save**
-
-The medatada will be re-detected and you will be able to see the list of reference sequences in the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop-down.
-
-
-
-
diff -r 060c2129612f -r 9eee08ea613b samtools/samtools_sort/samtools_sort.xml
--- a/samtools/samtools_sort/samtools_sort.xml Thu Oct 03 11:27:47 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,40 +0,0 @@
-
- BAM dataset
-
- macros.xml
-
-
-
-
- samtools sort $sort_mode -@ \${GALAXY_SLOTS:-1} -o "${output1}" -O bam -T dataset "${input1}"
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-**What it does**
-
-This tool uses ``samtools sort`` command to sort BAM datasets in coordinate or read name order.
-
-
-
-
-