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 ===================================== Binary files a/Docker/coverage and /dev/null differ ===================================== Docker/v2.3.0.tar.gz deleted ===================================== Binary files a/Docker/v2.3.0.tar.gz and /dev/null differ ===================================== 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 - ===================================== binaries/covtobed deleted ===================================== Binary files a/binaries/covtobed and /dev/null differ ===================================== binaries/covtobed_debug deleted ===================================== Binary files a/binaries/covtobed_debug and /dev/null differ ===================================== binaries/covtobed_mac deleted ===================================== Binary files a/binaries/covtobed_mac and /dev/null differ ===================================== binaries/covtobed_mac_debug deleted ===================================== Binary files a/binaries/covtobed_mac_debug and /dev/null differ 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 You're receiving this email because of your account on salsa.debian.org.
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