[med-svn] [salmon] 03/11: new upstream version
Sascha Steinbiss
satta at debian.org
Sat Sep 10 13:22:41 UTC 2016
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satta pushed a commit to branch master
in repository salmon.
commit 5ea5fb8ae322e4dd9a1c520e6c12b2db3a7c6c0a
Author: Sascha Steinbiss <satta at debian.org>
Date: Sat Sep 10 11:50:22 2016 +0000
new upstream version
---
debian/changelog | 7 +++++--
debian/patches/add_MEM_F_SELF_OVLP.patch | 4 ++--
debian/patches/cmake-typo-fixes | 2 +-
debian/patches/dependency-fix | 28 ++++++++++++-------------
debian/patches/disable-version-check | 2 +-
debian/patches/use_debian_packaged_rapmap.patch | 4 ++--
6 files changed, 25 insertions(+), 22 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index 5efebca..3f7e795 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,9 +1,12 @@
-salmon (0.7.1+ds1-1) UNRELEASED; urgency=medium
+salmon (0.7.2+ds1-1) unstable; urgency=medium
* Team upload
* New upstream version
+ * Make sure build uses Debian's packaged version of dependencies
+ (exception: RapMap, see below).
* d/watch: use xz compression
- TODO: package https://github.com/COMBINE-lab/RapMap
+ * Include necessary parts of RapMap code until upstream sorts out
+ code embedding.
-- Andreas Tille <tille at debian.org> Tue, 30 Aug 2016 09:10:48 +0200
diff --git a/debian/patches/add_MEM_F_SELF_OVLP.patch b/debian/patches/add_MEM_F_SELF_OVLP.patch
index 40dd0b7..af72306 100644
--- a/debian/patches/add_MEM_F_SELF_OVLP.patch
+++ b/debian/patches/add_MEM_F_SELF_OVLP.patch
@@ -13,8 +13,8 @@ Author: Sascha Steinbiss <sascha at steinbiss.name>
}
// Jellyfish 2 include
-@@ -125,6 +126,7 @@
- #include "SalmonOpts.hpp"
+@@ -128,6 +129,7 @@
+ #include "RapMapUtils.hpp"
//#include "TextBootstrapWriter.hpp"
+
diff --git a/debian/patches/cmake-typo-fixes b/debian/patches/cmake-typo-fixes
index 782a0df..8dbd663 100644
--- a/debian/patches/cmake-typo-fixes
+++ b/debian/patches/cmake-typo-fixes
@@ -2,7 +2,7 @@ Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Description: fix upstream's typos
--- a/src/SalmonQuantify.cpp
+++ b/src/SalmonQuantify.cpp
-@@ -1985,7 +1985,7 @@
+@@ -2088,7 +2088,7 @@
(
"maxOcc,m",
po::value<int>(&(memOptions->max_occ))->default_value(200),
diff --git a/debian/patches/dependency-fix b/debian/patches/dependency-fix
index 2f50a41..d85157b 100644
--- a/debian/patches/dependency-fix
+++ b/debian/patches/dependency-fix
@@ -333,11 +333,11 @@ Description: Use Debian version of dependencies, don't download them
-message("==================================================================")
-ExternalProject_Add(libstadenio
- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/staden-io_lib/releases/download/v1.13.10/io_lib-1.13.10.tar.gz -o staden-io_lib-v1.13.10.tar.gz &&
-- mkdir -p staden-io_lib-1.13.10 &&
-- tar -xzf staden-io_lib-v1.13.10.tar.gz --strip-components=1 -C staden-io_lib-1.13.10 &&
+- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/staden-io_lib/archive/v1.14.8.tar.gz -o staden-io_lib-v1.14.8.tar.gz &&
+- mkdir -p staden-io_lib-1.14.8 &&
+- tar -xzf staden-io_lib-v1.14.8.tar.gz --strip-components=1 -C staden-io_lib-1.14.8 &&
- rm -fr staden-io_lib &&
-- mv -f staden-io_lib-1.13.10 staden-io_lib
+- mv -f staden-io_lib-1.14.8 staden-io_lib
- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/staden-io_lib
- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
- CONFIGURE_COMMAND ./configure --enable-shared=no --without-libcurl --prefix=<INSTALL_DIR> LDFLAGS=${LIBSTADEN_LDFLAGS} CFLAGS=${LIBSTADEN_CFLAGS} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER}
@@ -351,10 +351,10 @@ Description: Use Debian version of dependencies, don't download them
-message("==================================================================")
-ExternalProject_Add(libspdlog
- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/spdlog/archive/v1.0.1.tar.gz -o spdlog-v1.0.1.tar.gz &&
-- tar -xzf spdlog-v1.0.1.tar.gz &&
+- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/spdlog/archive/v1.12.tar.gz -o spdlog-v1.12.tar.gz &&
+- tar -xzf spdlog-v1.12.tar.gz &&
- rm -fr spdlog &&
-- mv -f spdlog-1.0.1 spdlog
+- mv -f spdlog-1.12 spdlog
- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/spdlog
- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
- CONFIGURE_COMMAND ""
@@ -366,11 +366,11 @@ Description: Use Debian version of dependencies, don't download them
+#message("==================================================================")
+#ExternalProject_Add(libstadenio
+# DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-+# DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/staden-io_lib/releases/download/v1.13.10/io_lib-1.13.10.tar.gz -o staden-io_lib-v1.13.10.tar.gz &&
-+# mkdir -p staden-io_lib-1.13.10 &&
-+# tar -xzf staden-io_lib-v1.13.10.tar.gz --strip-components=1 -C staden-io_lib-1.13.10 &&
++# DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/staden-io_lib/archive/v1.14.8.tar.gz -o staden-io_lib-v1.14.8.tar.gz &&
++# mkdir -p staden-io_lib-1.14.8 &&
++# tar -xzf staden-io_lib-v1.14.8.tar.gz --strip-components=1 -C staden-io_lib-1.14.8 &&
+# rm -fr staden-io_lib &&
-+# mv -f staden-io_lib-1.13.10 staden-io_lib
++# mv -f staden-io_lib-1.14.8 staden-io_lib
+# SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/staden-io_lib
+# INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
+# CONFIGURE_COMMAND ./configure --enable-shared=no --without-libcurl --prefix=<INSTALL_DIR> LDFLAGS=${LIBSTADEN_LDFLAGS} CFLAGS=${LIBSTADEN_CFLAGS} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER}
@@ -384,10 +384,10 @@ Description: Use Debian version of dependencies, don't download them
+#message("==================================================================")
+#ExternalProject_Add(libspdlog
+# DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-+# DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/spdlog/archive/v1.0.1.tar.gz -o spdlog-v1.0.1.tar.gz &&
-+# tar -xzf spdlog-v1.0.1.tar.gz &&
++# DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/spdlog/archive/v1.12.tar.gz -o spdlog-v1.12.tar.gz &&
++# tar -xzf spdlog-v1.12.tar.gz &&
+# rm -fr spdlog &&
-+# mv -f spdlog-1.0.1 spdlog
++# mv -f spdlog-1.12 spdlog
+# SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/spdlog
+# INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
+# CONFIGURE_COMMAND ""
diff --git a/debian/patches/disable-version-check b/debian/patches/disable-version-check
index 0c3eb70..6712c6b 100644
--- a/debian/patches/disable-version-check
+++ b/debian/patches/disable-version-check
@@ -2,7 +2,7 @@ Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Description: Disable the newer version check
--- a/src/Salmon.cpp
+++ b/src/Salmon.cpp
-@@ -181,10 +181,10 @@ int main( int argc, char* argv[] ) {
+@@ -179,10 +179,10 @@
std::exit(0);
}
diff --git a/debian/patches/use_debian_packaged_rapmap.patch b/debian/patches/use_debian_packaged_rapmap.patch
index 98303f2..ffc288c 100644
--- a/debian/patches/use_debian_packaged_rapmap.patch
+++ b/debian/patches/use_debian_packaged_rapmap.patch
@@ -23,8 +23,8 @@
CollapsedEMOptimizer.cpp
CollapsedGibbsSampler.cpp
Salmon.cpp
-@@ -39,7 +30,6 @@
- StadenUtils.cpp
+@@ -38,7 +29,6 @@
+ SequenceBiasModel.cpp
TranscriptGroup.cpp
GZipWriter.cpp
-#${GAT_SOURCE_DIR}/external/install/src/rapmap/sais.c
--
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