Commit 61d0d1c5 authored by Shayan Doust's avatar Shayan Doust
Browse files

2to3 patch for simkamin and create second package

parent 253f5a2c

debian/control

+24 −6
Original line number Diff line number Diff line
@@ -8,7 +8,9 @@ Build-Depends: debhelper-compat (= 12), 
               libgatbcore-dev,

               zlib1g-dev,

               libhdf5-dev,

	       libboost-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
@@ -23,3 +25,19 @@ 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 → 100644
+38 −0
Original line number Diff line number Diff line 
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 −0
Original line number Diff line number Diff line 
2to3.patch

use_debian_packaged_libraries.patch

debian/rules

+3 −2
Original line number Diff line number Diff line
@@ -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/*