[med-svn] [Git][med-team/tiddit][master] 5 commits: d/watch: Fix watch regex
Nilesh Patra (@nilesh)
gitlab at salsa.debian.org
Thu Jun 3 21:09:37 BST 2021
Nilesh Patra pushed to branch master at Debian Med / tiddit
Commits:
ddf32d81 by Nilesh Patra at 2021-06-04T01:31:00+05:30
d/watch: Fix watch regex
- - - - -
dd8fe12d by Nilesh Patra at 2021-06-04T01:31:32+05:30
New upstream version 2.12.1+dfsg
- - - - -
4cb83ad4 by Nilesh Patra at 2021-06-04T01:31:33+05:30
Update upstream source from tag 'upstream/2.12.1+dfsg'
Update to upstream version '2.12.1+dfsg'
with Debian dir 5aef6248749e72b7c0c872520900049984fc2849
- - - - -
d3049902 by Nilesh Patra at 2021-06-04T01:33:33+05:30
Declare compliance with policy 4.5.1
- - - - -
e4bdf4c1 by Nilesh Patra at 2021-06-04T01:39:11+05:30
Interim changelog entry
- - - - -
8 changed files:
- + Dockerfile
- README.md
- TIDDIT.py
- debian/changelog
- debian/control
- debian/watch
- src/TIDDIT.cpp
- + versioned_singularity/TIDDIT.2.12.1
Changes:
=====================================
Dockerfile
=====================================
@@ -0,0 +1,55 @@
+FROM python:3.8-slim
+
+RUN apt-get update && \
+ apt-get upgrade -y && \
+ apt-get install -y \
+ autoconf \
+ automake \
+ build-essential \
+ cmake \
+ libbz2-dev \
+ libcurl4-gnutls-dev \
+ liblzma-dev \
+ libncurses5-dev \
+ libssl-dev \
+ make \
+ unzip \
+ wget \
+ zlib1g-dev && \
+ apt-get clean && \
+ apt-get purge && \
+ rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
+WORKDIR /app
+
+## Install samtools for cram processing
+RUN wget --no-verbose https://github.com/samtools/samtools/releases/download/1.10/samtools-1.10.tar.bz2 && \
+ bunzip2 samtools-1.10.tar.bz2 && \
+ tar -xf samtools-1.10.tar && \
+ cd samtools-1.10 && \
+ ./configure && \
+ make all all-htslib && \
+ make install install-htslib && \
+ rm /app/samtools-1.10.tar
+
+## Set TIDDIT version
+ARG TIDDIT_VERSION=2.12.0
+
+## Add some info
+LABEL base_image="python:3.8-slim"
+LABEL software="TIDDIT.py"
+LABEL software.version=${TIDDIT_VERSION}
+
+## Download and extract
+RUN wget https://github.com/SciLifeLab/TIDDIT/archive/TIDDIT-${TIDDIT_VERSION}.zip && \
+ unzip TIDDIT-${TIDDIT_VERSION}.zip && \
+ rm TIDDIT-${TIDDIT_VERSION}.zip
+
+## Install
+RUN cd TIDDIT-TIDDIT-${TIDDIT_VERSION} && \
+ ./INSTALL.sh && \
+ chmod +x /app/TIDDIT-TIDDIT-${TIDDIT_VERSION}/TIDDIT.py && \
+ ln -s /app/TIDDIT-TIDDIT-${TIDDIT_VERSION}/TIDDIT.py /usr/local/bin
+
+ENTRYPOINT ["TIDDIT.py"]
+CMD ["--help"]
=====================================
README.md
=====================================
@@ -83,28 +83,56 @@ The reference is required for analysing cram files.
NOTE: It is important that you use the TIDDIT.py wrapper for SV detection. The TIDDIT binary in the TIDDIT/bin folder does not perform any clustering, it simply extract SV signatures into a tab file.
-TIDDIT may be fine tuned by altering these optional parameters:
-
- -o - The prefix of the output files(default = output)
-
- -i - The maximum allowed insert size of a normal pair. Pairs having larger insert
- than this is treated as discordant pairs. Default is 99.9th percentile + 100 bp
-
- -d - The pair orientation, use this setting to override the automatic orientation selection
-
- -l - The density parameter, to create a cluster, more than l signals (split reads+ discordant pairs) must be present, signals are added to a cluster if they are neighbouring atleast this number of signals (defualt 3, minimum 2)
-
- -p - The minimum number of discordant pairs and supplementary alignments used to call large SV. Default is 3
-
- -r - The minimum number of supplementary alignments used to call small SV. Default is 3
-
- -q - The minimum mapping quality of the discordant pairs/supplementary alignments
- forming a variant. Default value is 5.
- -n - The ploidy of the organism ,(default = 2)
+TIDDIT may be fine-tuned by altering these optional parameters:
+
+ -o output prefix(default=output)
+
+ -i paired reads maximum allowed insert size. Pairs aligning
+ on the same chr at a distance higher than this are
+ considered candidates for SV (default= 99.9th percentile of insert size)
+
+ -d expected reads orientations, possible values "innie" (-> <-) or "outtie" (<- ->).
+ Default: major orientation within the dataset
+
+ -p Minimum number of supporting pairs in order to call a variation event (default 3)
+
+ -r Minimum number of supporting split reads to call a small variant (default 3)
+
+ -q Minimum mapping quality to consider an alignment (default= 5)
+
+ -Q Minimum regional mapping quality (default 20)
+
+ -n the ploidy of the organism,(default = 2)
+
+ -e clustering distance parameter, discordant pairs closer
+ than this distance are considered to belong to the same
+ variant(default = sqrt(insert-size*2)*12)
+
+ -l min-pts parameter (default=3),must be set >= 2
+
+ -s Number of reads to sample when computing library statistics(default=25000000)
+
+ -z minimum variant size (default=100), variants smaller than
+ this will not be printed ( z < 10 is not recomended)
+
+ --force_ploidy force the ploidy to be set to -n across the entire genome
+ (i.e skip coverage normalisation of chromosomes)
+
+ --no_cluster Run only the TIDDIT signal extraction
+
+ --debug rerun the tiddit clustering procedure
+
+ --n_mask exclude regions from coverage calculation if they contain more than this fraction of N (default = 0.5)
+
+ --ref reference fasta, used for GC correction and for reading cram
+
+ --p_ratio minimum discordant pair/normal pair ratio at the breakpoint junction(default=0.2)
+
+ --r_ratio minimum split read/coverage ratio at the breakpoint junction(default=0.1)
+
+
- --force_ploidy - set the ploidy of all chromosomes to -n (including the sex chromosomes), this option will disable the ploidy estimation.
- This option is meant to be used for low quality data or for species having equal ploidy across all chromosomes
output:
=====================================
TIDDIT.py
=====================================
@@ -8,7 +8,7 @@ wd=os.path.dirname(os.path.realpath(__file__))
sys.path.insert(0, '{}/src/'.format(wd))
import TIDDIT_calling
-version = "2.12.0"
+version = "2.12.1"
parser = argparse.ArgumentParser("""TIDDIT-{}""".format(version),add_help=False)
parser.add_argument('--sv' , help="call structural variation", required=False, action="store_true")
parser.add_argument('--cov' , help="generate a coverage bed file", required=False, action="store_true")
@@ -35,8 +35,8 @@ if args.sv:
parser.add_argument('--debug',action="store_true", help="rerun the tiddit clustering procedure")
parser.add_argument('--n_mask',type=float,default=0.5, help="exclude regions from coverage calculation if they contain more than this fraction of N (default = 0.5)")
parser.add_argument('--ref', type=str, help="reference fasta, used for GC correction and for reading cram")
- parser.add_argument('--p_ratio', type=float,default=0.2, help="minimum discordant pair/normal pair ratio at the breakpoint junction(default=20%)")
- parser.add_argument('--r_ratio', type=float,default=0.1, help="minimum split read/coverage ratio at the breakpoint junction(default=10%)")
+ parser.add_argument('--p_ratio', type=float,default=0.2, help="minimum discordant pair/normal pair ratio at the breakpoint junction(default=0.2)")
+ parser.add_argument('--r_ratio', type=float,default=0.1, help="minimum split read/coverage ratio at the breakpoint junction(default=0.1)")
args= parser.parse_args()
args.wd=os.path.dirname(os.path.realpath(__file__))
=====================================
debian/changelog
=====================================
@@ -1,3 +1,16 @@
+tiddit (2.12.1+dfsg-1) UNRELEASED; urgency=medium
+
+ * Team Upload.
+ [ Steffen Möller ]
+ * Update metadata - added ref to bio.tools
+
+ [ Nilesh Patra ]
+ * d/watch: Fix watch regex
+ * New upstream version 2.12.1+dfsg
+ * Declare compliance with policy 4.5.1
+
+ -- Nilesh Patra <nilesh at debian.org> Fri, 04 Jun 2021 01:33:49 +0530
+
tiddit (2.12.0+dfsg-3) unstable; urgency=medium
* Team Upload.
=====================================
debian/control
=====================================
@@ -10,7 +10,7 @@ Build-Depends: debhelper-compat (= 13),
python3-dev,
libbamtools-dev (>= 2.5.1+dfsg-6),
zlib1g-dev
-Standards-Version: 4.5.0
+Standards-Version: 4.5.1
Vcs-Browser: https://salsa.debian.org/med-team/tiddit
Vcs-Git: https://salsa.debian.org/med-team/tiddit.git
Homepage: https://github.com/SciLifeLab/TIDDIT
=====================================
debian/watch
=====================================
@@ -1,4 +1,4 @@
version=4
opts="repacksuffix=+dfsg,dversionmangle=auto,repack,compression=xz,filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE at -$1.tar.gz%" \
-https://github.com/SciLifeLab/TIDDIT/releases .*/archive/TIDDIT- at ANY_VERSION@\.tar\.gz
+https://github.com/SciLifeLab/TIDDIT/releases .*/archive/.*/TIDDIT- at ANY_VERSION@\.tar\.gz
=====================================
src/TIDDIT.cpp
=====================================
@@ -46,7 +46,7 @@ int main(int argc, char **argv) {
int min_variant_size= 100;
int sample = 100000000;
string outputFileHeader ="output";
- string version = "2.12.0";
+ string version = "2.12.1";
//collect all options as a vector
vector<string> arguments(argv, argv + argc);
=====================================
versioned_singularity/TIDDIT.2.12.1
=====================================
@@ -0,0 +1,23 @@
+BootStrap: debootstrap
+OSVersion: trusty
+MirrorURL: http://us.archive.ubuntu.com/ubuntu/
+
+
+%runscript
+ echo "This is what happens when you run the container..."
+
+
+%post
+ echo "Hello from inside the container"
+ sed -i 's/$/ universe/' /etc/apt/sources.list
+ apt-get update
+ apt-get -y --force-yes install build-essential cmake make zlib1g-dev python python-dev python-setuptools git wget libbz2-dev unzip
+ easy_install pip
+ pip install numpy cython
+
+ wget https://github.com/SciLifeLab/TIDDIT/archive/TIDDIT-2.12.1.zip
+ unzip TIDDIT-2.12.1.zip
+
+ mv TIDDIT-TIDDIT-2.12.1/* /bin/
+ cd /bin/ && ./INSTALL.sh
+ chmod +x /bin/TIDDIT.py
View it on GitLab: https://salsa.debian.org/med-team/tiddit/-/compare/1337afa9fab96ad438a3b7cd88a46e17101f756e...e4bdf4c1cb193eee4903560e3e2dbec169c08bd6
--
View it on GitLab: https://salsa.debian.org/med-team/tiddit/-/compare/1337afa9fab96ad438a3b7cd88a46e17101f756e...e4bdf4c1cb193eee4903560e3e2dbec169c08bd6
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