Shayan Doust pushed to branch master at Debian Med / simka
Commits: 61d0d1c5 by Shayan Doust at 2019-09-12T02:35:03Z 2to3 patch for simkamin and create second package - - - - - 4 changed files: - debian/control - + debian/patches/2to3.patch - debian/patches/series - debian/rules Changes: ===================================== debian/control ===================================== @@ -4,11 +4,13 @@ Uploaders: Shayan Doust <[email protected]> Section: science Priority: optional Build-Depends: debhelper-compat (= 12), - cmake, - libgatbcore-dev, - zlib1g-dev, - libhdf5-dev, - libboost-dev + cmake, + libgatbcore-dev, + zlib1g-dev, + libhdf5-dev, + libboost-dev, + python3-all, + dh-python Standards-Version: 4.4.0 Vcs-Browser: https://salsa.debian.org/med-team/simka Vcs-Git: https://salsa.debian.org/med-team/simka.git @@ -18,8 +20,24 @@ Package: simka Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends}, - libgatbcore2 + libgatbcore2 Description: comparative metagenomics method dedicated to NGS datasets Simka is a de novo comparative metagenomics tool. Simka represents each dataset as a k-mer spectrum and compute several classical ecological distances between them. + +Package: simkamin +Architecture: all +Depends: ${python3:Depends}, + ${misc:Depends}, + python3 +Description: comparative metagenomics method dedicated to NGS datasets + Simka is a de novo comparative metagenomics tool. Simka represents each + dataset as a k-mer spectrum and compute several classical ecological + distances between them. + . + The difference with Simka stands in the fact that SimkaMin outputs + approximate (but very similar) results by subsampling the kmer space. + With this strategy, and with default parameters, SimkaMin is an order + of magnitude faster, uses 10 times less memory and 70 times less disk + than Simka. ===================================== debian/patches/2to3.patch ===================================== @@ -0,0 +1,38 @@ +diff --git a/simkaMin/simkaMin.py b/simkaMin/simkaMin.py +index 320d6e2..c0fa28d 100755 +--- a/simkaMin/simkaMin.py ++++ b/simkaMin/simkaMin.py +@@ -69,7 +69,7 @@ simkaMinCoreBin=args.bin + if args.bin is not None: + # given by the user + if not is_executable(simkaMinCoreBin): +- print("Error: "+simkaMinCoreBin+" not found or not executable, should be <SimkaDirectory>/build/bin/simkaMinCore") ++ print(("Error: "+simkaMinCoreBin+" not found or not executable, should be <SimkaDirectory>/build/bin/simkaMinCore")) + exit(1) + else: + # Check if is in the PATH +@@ -198,4 +198,4 @@ ret = os.system(exportCommand) + if ret != 0: print("ERROR"); exit(1) + + print("\n\n") +-print("Result dir: " + args.out) ++print(("Result dir: " + args.out)) +diff --git a/simkaMin/simkaMin_update.py b/simkaMin/simkaMin_update.py +index 99968d0..c5bc0ad 100755 +--- a/simkaMin/simkaMin_update.py ++++ b/simkaMin/simkaMin_update.py +@@ -67,7 +67,7 @@ simkaMinCoreBin=args.bin + if args.bin is not None: + # given by the user + if not is_executable(simkaMinCoreBin): +- print("Error: "+simkaMinCoreBin+" not found or not executable, should be <SimkaDirectory>/build/bin/simkaMinCore") ++ print(("Error: "+simkaMinCoreBin+" not found or not executable, should be <SimkaDirectory>/build/bin/simkaMinCore")) + exit(1) + else: + # Check if is in the PATH +@@ -219,4 +219,4 @@ shutil.rmtree(distanceDir_newVsNew) + os.remove(sketchFilename_new) + + print("\n\n") +-print("Result dir: " + existingDir) ++print(("Result dir: " + existingDir)) ===================================== debian/patches/series ===================================== @@ -1 +1,2 @@ +2to3.patch use_debian_packaged_libraries.patch ===================================== debian/rules ===================================== @@ -13,5 +13,6 @@ include /usr/share/dpkg/default.mk override_dh_install: dh_install - rm -r debian/simka/usr/example - chrpath --delete debian/simka/usr/bin/* + rm -r debian/tmp/usr/example \ + debian/tmp/usr/scripts + chrpath --delete debian/tmp/usr/bin/* View it on GitLab: https://salsa.debian.org/med-team/simka/commit/61d0d1c5200382b6c7cd5a3fec611c0eb095dfeb -- View it on GitLab: https://salsa.debian.org/med-team/simka/commit/61d0d1c5200382b6c7cd5a3fec611c0eb095dfeb You're receiving this email because of your account on salsa.debian.org.
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