[med-svn] [Git][med-team/tiddit][upstream] New upstream version 2.12.2+dfsg

[Nilesh Patra (@nilesh)]

Nilesh Patra pushed to branch upstream at Debian Med / tiddit


Commits:
fe9b8ed0 by Nilesh Patra at 2021-11-03T20:56:42+05:30
New upstream version 2.12.2+dfsg
- - - - -


6 changed files:

- Dockerfile
- Singularity
- TIDDIT.py
- 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")


=====================================
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/-/commit/fe9b8ed0bb06b3953669c56fdcbe9e0ff0e17c44

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View it on GitLab: https://salsa.debian.org/med-team/tiddit/-/commit/fe9b8ed0bb06b3953669c56fdcbe9e0ff0e17c44
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