[med-svn] [Git][med-team/tiddit][master] 4 commits: New upstream version 2.12.2+dfsg
Nilesh Patra (@nilesh)
gitlab at salsa.debian.org
Wed Nov 3 16:06:02 GMT 2021
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 <nilesh at debian.org> 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 <nilesh at debian.org>
-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
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