progress on #434 Kraken2

434_Kraken2/Kraken2-2.1.3-gompi-2023a.eb

@@ -19,15 +19,13 @@ toolchainopts = {'openmp': True, 'cstd': 'c++11'}
 github_account = 'DerrickWood'
 source_urls = [GITHUB_LOWER_SOURCE]
 sources = ['v%(version)s.tar.gz']
-patches = [  # TODO
-    '%(name)s-2.1.1_fix_installation_for_easybuild.patch',
-    '%(name)s-%(version)s_fix_ncbi_https_server.patch',
+patches = [
+    '%(name)s-2.1.3_fix_installation_for_easybuild.patch',
 ]
-checksums = [  # TODO
-    'e5f431e8bc3d5493a79e1d8125f4aacbad24f9ea2cc9657b66da06a32bef6ff3',  # v2.1.2.tar.gz
-    # Kraken2-2.1.1_fix_installation_for_easybuild.patch
-    '5ea9093becbdf7705a29fd2e56050118700c850ac5374aae5ee9b5e5924d3a11',
-    '8db78096340352e97589a189a86a020ff31bd60f0c332a1794d532fabd5bd116',  # Kraken2-2.1.2_fix_ncbi_https_server.patch
+checksums = [
+    {'v2.1.3.tar.gz': '5269fa14adfb02e38c2da2e605e909a432d76c680d73e2e0e80e27ccd04d7c69'},
+    {'Kraken2-2.1.3_fix_installation_for_easybuild.patch':
+     'd2faecff258133033cb81d5ac70d1a7ff1b4323091411aa835a13de83f2cc174'},
 ]
 
 dependencies = [

434_Kraken2/Kraken2-2.1.3_fix_installation_for_easybuild.patch

@@ -0,0 +1,30 @@
+Fix install script and src/Makefile for EasyBuild.
+
+Åke Sandgren, 2021-04-30
+Update: Petr Král (INUITS)
+diff -u install_kraken2.sh.orig install_kraken2.sh
+--- install_kraken2.sh.orig     2023-06-07 02:25:37.000000000 +0200
++++ install_kraken2.sh  2024-11-12 11:34:20.122193572 +0100
+@@ -23,7 +23,9 @@
+
+ # Perl cmd used to canonicalize dirname - "readlink -f" doesn't work
+ # on OS X.
+-export KRAKEN2_DIR=$(perl -MCwd=abs_path -le 'print abs_path(shift)' "$1")
++# export KRAKEN2_DIR=$(perl -MCwd=abs_path -le 'print abs_path(shift)' "$1")
++
++export KRAKEN2_DIR=$1
+
+ mkdir -p "$KRAKEN2_DIR"
+ make -C src install
+diff -u src/Makefile.orig src/Makefile
+--- src/Makefile.orig   2023-06-07 02:25:37.000000000 +0200
++++ src/Makefile        2024-11-12 10:13:26.330138787 +0100
+@@ -1,6 +1,6 @@
+-CXX = g++
++CXX ?= g++
+ KRAKEN2_SKIP_FOPENMP ?= -fopenmp
+-CXXFLAGS = $(KRAKEN2_SKIP_FOPENMP) -Wall -std=c++11 -O3
++CXXFLAGS ?= $(KRAKEN2_SKIP_FOPENMP) -Wall -std=c++11 -O3
+ CXXFLAGS += -DLINEAR_PROBING
+
+ .PHONY: all clean install