[med-svn] [Git][med-team/simka][master] 2to3 patch for simkamin and create second package

[Shayan Doust]

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 <hello at shayandoust.me>
 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
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