[med-svn] [Git][med-team/covtobed][upstream] New upstream version 1.1.2+dfsg

[Shayan Doust]

Shayan Doust pushed to branch upstream at Debian Med / covtobed


Commits:
78e1536e by Shayan Doust at 2020-06-02T18:41:45+01:00
New upstream version 1.1.2+dfsg
- - - - -


10 changed files:

- − Docker/README.md
- − Docker/coverage
- − Docker/v2.3.0.tar.gz
- − binaries/README.md
- − binaries/build_osx.sh
- − binaries/build_ubuntu.sh
- − binaries/covtobed
- − binaries/covtobed_debug
- − binaries/covtobed_mac
- − binaries/covtobed_mac_debug


Changes:

=====================================
Docker/README.md deleted
=====================================
@@ -1,20 +0,0 @@
-# Docker container
-
-This directories contains files to generate the Docker/Singularity images that provide:
-
-* `covtobed` as described in the [README](../README.md)
-* `coverage` a legacy program with some more features that has been used for the EU project _MD-PAEDIGREE_.
- 
-## How to get it
- 
-The Docker image is distributed via [Docker Hub](https://hub.docker.com/r/andreatelatin/covtobed):
- 
-```bash
-sudo docker pull andreatelatin/covtobed
-```
- 
-The Singularity image can be pulled from Docker Hub as well. A snapshot (v. 0.3) is available from [Zenodo](https://zenodo.org/record/1063493):
-
-```bash
-singularity pull andreatelatin/covtobed
-```


=====================================
Docker/coverage deleted
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=====================================
Docker/v2.3.0.tar.gz deleted
=====================================
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=====================================
binaries/README.md deleted
=====================================
@@ -1,6 +0,0 @@
-# Precompiled binaries for Linux and OS X
-
-* Linux: [https://github.com/telatin/covtobed/releases/download/v0.3/covtobed](https://github.com/telatin/covtobed/releases/download/v0.3/covtobed)
-* OS X: [https://github.com/telatin/covtobed/releases/download/v0.3/covtobed_osx](https://github.com/telatin/covtobed/releases/download/v0.3/covtobed_osx)
-
-The Linux binary has been tested with Ubuntu 14.04, Ubuntu 18.04, Fedora 26 and Fedora 30.


=====================================
binaries/build_osx.sh deleted
=====================================
@@ -1,23 +0,0 @@
-#!/bin/bash
-if [ ! -d "$HOME/miniconda3" ]; then
-	echo "MINICONDA not found in $HOME/miniconda3"
-	exit 1;
-fi
-if [ ! -e "$HOME/miniconda3/lib/libbamtools.a" ]; then
-	echo "'$HOME/miniconda3/lib/libbamtools.a' not found"
-	exit 2;
-fi
-
-set -euxo pipefail
-
-SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null && pwd )"
-cd "$SCRIPT_DIR/.."
-
-sed -i.bak 's/#define debug if(.*)/#define debug if(true)/' base.cpp
-c++ -std=c++11 ./*.cpp -I"${HOME}"/miniconda3/include/bamtools/ -L$"{HOME}"/miniconda3/lib/ "$HOME"/miniconda3/lib/libbamtools.a  \
- -o binaries/covtobed_mac_debug -lz
-
-sed -i.bak 's/#define debug if(.*)/#define debug if(false)/' base.cpp
-c++ -std=c++11 ./*.cpp -I"${HOME}"/miniconda3/include/bamtools/ -L"${HOME}"/miniconda3/lib/ "$HOME"/miniconda3/lib/libbamtools.a  \
- -o binaries/covtobed_mac -lz
-cd -


=====================================
binaries/build_ubuntu.sh deleted
=====================================
@@ -1,18 +0,0 @@
-#!/bin/bash
-
-set -euxo pipefail
-SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null && pwd )"
-cd "$SCRIPT_DIR/.."
-
-
-# Make DEBUG
-sed -i 's/#define debug if(.*)/#define debug if(true)/' base.cpp
-c++ -std=c++11 ./*.cpp  -I/usr/include/bamtools /usr/lib/x86_64-linux-gnu/libbamtools.a  /usr/lib/gcc/x86_64-linux-gnu/5/libstdc++.a \
- -o binaries/covtobed_debug -lz
-
-
-# Make NORMAL
-sed -i 's/#define debug if(.*)/#define debug if(false)/' base.cpp
-c++ -std=c++11 ./*.cpp  -I/usr/include/bamtools /usr/lib/x86_64-linux-gnu/libbamtools.a  /usr/lib/gcc/x86_64-linux-gnu/5/libstdc++.a \
- -o binaries/covtobed -lz
-cd -


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binaries/covtobed_debug deleted
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binaries/covtobed_mac deleted
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View it on GitLab: https://salsa.debian.org/med-team/covtobed/-/commit/78e1536e9f995a857dc3eeeb05027c5dacc594b5

-- 
View it on GitLab: https://salsa.debian.org/med-team/covtobed/-/commit/78e1536e9f995a857dc3eeeb05027c5dacc594b5
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