Nilesh Patra pushed to branch master at Debian Med / tiddit
Commits: fe9b8ed0 by Nilesh Patra at 2021-11-03T20:56:42+05:30 New upstream version 2.12.2+dfsg - - - - - 5d899db6 by Nilesh Patra at 2021-11-03T20:56:43+05:30 Update upstream source from tag 'upstream/2.12.2+dfsg' Update to upstream version '2.12.2+dfsg' with Debian dir ae10d468f2e380a5c2c87b4d236f3ff59affa958 - - - - - d3c64c6f by Nilesh Patra at 2021-11-03T20:57:28+05:30 Remove remove-unused-function.patch, merged upstream - - - - - 6dd52b11 by Nilesh Patra at 2021-11-03T20:58:13+05:30 Upload to unstable - - - - - 9 changed files: - Dockerfile - Singularity - TIDDIT.py - debian/changelog - − debian/patches/remove-unused-function.patch - debian/patches/series - src/TIDDIT.cpp - src/data_structures/Translocation.cpp - versioned_singularity/TIDDIT.2.12.1 Changes: ===================================== Dockerfile ===================================== @@ -33,7 +33,7 @@ RUN wget --no-verbose https://github.com/samtools/samtools/releases/download/1.1 rm /app/samtools-1.10.tar ## Set TIDDIT version -ARG TIDDIT_VERSION=2.12.0 +ARG TIDDIT_VERSION=2.12.1 ## Add some info LABEL base_image="python:3.8-slim" ===================================== Singularity ===================================== @@ -2,18 +2,30 @@ BootStrap: debootstrap OSVersion: trusty MirrorURL: http://us.archive.ubuntu.com/ubuntu/ +%environment + SHELL=/bin/bash + PATH=/opt/anaconda/bin:${PATH} + %runscript echo "This is what happens when you run the container..." - + PATH=/opt/anaconda/bin:${PATH} + echo "This is what happens when you run the container..." %post echo "Hello from inside the container" sed -i 's/$/ universe/' /etc/apt/sources.list apt-get update apt-get upgrade - apt-get -y --force-yes install build-essential cmake make zlib1g-dev python python-dev python-setuptools git - easy_install pip + apt-get -y --force-yes install build-essential cmake make zlib1g-dev python python-dev python-setuptools git wget + + cd /root/ && wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh + cd /root/ && chmod 700 ./Miniconda3-latest-Linux-x86_64.sh + cd /root/ && bash ./Miniconda3-latest-Linux-x86_64.sh -b -p /opt/anaconda/ + + export PATH=/opt/anaconda/bin:${PATH} + + pip install numpy cython git clone https://github.com/SciLifeLab/TIDDIT.git ===================================== 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 = "2.12.1" +version = "2.12.2" 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") ===================================== debian/changelog ===================================== @@ -1,3 +1,11 @@ +tiddit (2.12.2+dfsg-1) unstable; urgency=medium + + * Team Upload. + * New upstream version 2.12.2+dfsg + * Remove remove-unused-function.patch, merged upstream + + -- Nilesh Patra <[email protected]> Wed, 03 Nov 2021 20:57:43 +0530 + tiddit (2.12.1+dfsg-2) unstable; urgency=medium * Team Upload. ===================================== debian/patches/remove-unused-function.patch deleted ===================================== @@ -1,19 +0,0 @@ -Description: Remove unused int2str function -Author: Nilesh Patra <[email protected]> -Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=997258 -Forwarded: https://github.com/SciLifeLab/TIDDIT/issues/80 -Last-Update: 2021-10-31 ---- a/src/data_structures/Translocation.cpp -+++ b/src/data_structures/Translocation.cpp -@@ -9,11 +9,6 @@ - #include <string> - #include <cmath> - --string int2str(int to_be_converted){ -- string converted= static_cast<ostringstream*>( &(ostringstream() << to_be_converted) )->str(); -- return(converted); --} -- - void Window::initTrans(SamHeader head) { - uint32_t contigsNumber = 0; - SamSequenceDictionary sequences = head.Sequences; ===================================== debian/patches/series ===================================== @@ -1,3 +1,2 @@ use_debian_packaged_libs.patch Fix-tiddit-binary-location.patch -remove-unused-function.patch ===================================== 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 = "2.12.1"; + string version = "2.12.2"; //collect all options as a vector vector<string> arguments(argv, argv + argc); ===================================== src/data_structures/Translocation.cpp ===================================== @@ -9,11 +9,6 @@ #include <string> #include <cmath> -string int2str(int to_be_converted){ - string converted= static_cast<ostringstream*>( &(ostringstream() << to_be_converted) )->str(); - return(converted); -} - void Window::initTrans(SamHeader head) { uint32_t contigsNumber = 0; SamSequenceDictionary sequences = head.Sequences; ===================================== versioned_singularity/TIDDIT.2.12.1 ===================================== @@ -2,8 +2,13 @@ BootStrap: debootstrap OSVersion: trusty MirrorURL: http://us.archive.ubuntu.com/ubuntu/ +%environment + SHELL=/bin/bash + PATH=/opt/anaconda/bin:${PATH} %runscript + alias python=python3 + PATH=/opt/anaconda/bin:${PATH} echo "This is what happens when you run the container..." @@ -11,8 +16,15 @@ MirrorURL: http://us.archive.ubuntu.com/ubuntu/ echo "Hello from inside the container" sed -i 's/$/ universe/' /etc/apt/sources.list apt-get update + apt-get upgrade apt-get -y --force-yes install build-essential cmake make zlib1g-dev python python-dev python-setuptools git wget libbz2-dev unzip - easy_install pip + + cd /root/ && wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh + cd /root/ && chmod 700 ./Miniconda3-latest-Linux-x86_64.sh + cd /root/ && bash ./Miniconda3-latest-Linux-x86_64.sh -b -p /opt/anaconda/ + + export PATH=/opt/anaconda/bin:${PATH} + pip install numpy cython wget https://github.com/SciLifeLab/TIDDIT/archive/TIDDIT-2.12.1.zip View it on GitLab: https://salsa.debian.org/med-team/tiddit/-/compare/4a9352f45ef27da81058244cc0eef0309a9d66e2...6dd52b114b795fb47b9971d5f67ce9477ee87800 -- View it on GitLab: https://salsa.debian.org/med-team/tiddit/-/compare/4a9352f45ef27da81058244cc0eef0309a9d66e2...6dd52b114b795fb47b9971d5f67ce9477ee87800 You're receiving this email because of your account on salsa.debian.org.
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