[med-svn] [Git][med-team/covtobed][master] 3 commits: New upstream version 1.1.2+dfsg
Shayan Doust
gitlab at salsa.debian.org
Tue Jun 2 18:43:10 BST 2020
Shayan Doust pushed to branch master at Debian Med / covtobed
Commits:
78e1536e by Shayan Doust at 2020-06-02T18:41:45+01:00
New upstream version 1.1.2+dfsg
- - - - -
69dbdc2a by Shayan Doust at 2020-06-02T18:42:11+01:00
Update upstream source from tag 'upstream/1.1.2+dfsg'
Update to upstream version '1.1.2+dfsg'
with Debian dir 2e321ae32a7b89c5b1db613bc1721300c65bb862
- - - - -
44e2e1f0 by Shayan Doust at 2020-06-02T18:42:59+01:00
Repack to 1.1.2+dfsg
- - - - -
13 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
- debian/changelog
- debian/copyright
- debian/watch
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
=====================================
debian/changelog
=====================================
@@ -1,4 +1,4 @@
-covtobed (1.1.2-1) UNRELEASED; urgency=medium
+covtobed (1.1.2+dfsg-1) UNRELEASED; urgency=medium
* Initial release (Closes: #<bug>)
=====================================
debian/copyright
=====================================
@@ -1,11 +1,10 @@
Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: covtobed
-Source: <path_to_download>
-Comment: **** Before manually editing this file you should give ****
- scan-copyrights
- **** available in cme + lib-config-model-dpkg-perl ****
- **** package a try. For existing copyright files try ****
- cme update dpkg-copyright
+Source: https://github.com/telatin/covtobed
+Comment: Directories not needed as they contain pre-compiled binaries
+Files-Excluded:
+ Docker
+ binaries
Files: *
Copyright: 20xx-20yy <upstream>
=====================================
debian/watch
=====================================
@@ -1,4 +1,7 @@
version=4
-opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE at -$1.tar.gz%" \
+opts=\
+repacksuffix=+dfsg,\
+repack,compression=xz,\
+filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE at -$1.tar.gz% \
https://github.com/telatin/covtobed/releases .*/archive/v?@ANY_VERSION@\.tar\.gz
View it on GitLab: https://salsa.debian.org/med-team/covtobed/-/compare/f26703c2fa93b0b28b679e1adffd57c49ff8d2a2...44e2e1f071b6d781407dee91cc1fc6952a90fe5e
--
View it on GitLab: https://salsa.debian.org/med-team/covtobed/-/compare/f26703c2fa93b0b28b679e1adffd57c49ff8d2a2...44e2e1f071b6d781407dee91cc1fc6952a90fe5e
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