Merge pull request easybuilders#21489 from boegel/20240927141930_new_…

…pr_Cufflinks20190706

{bio}[GCC/12.3.0] Cufflinks v20190706, Boost v1.75.0

easybuild/easyconfigs/b/Boost/Boost-1.75.0-GCC-12.3.0.eb

@@ -0,0 +1,28 @@
+name = 'Boost'
+version = '1.75.0'
+
+homepage = 'https://www.boost.org/'
+description = """Boost provides free peer-reviewed portable C++ source libraries."""
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/']
+sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))]
+checksums = ['aeb26f80e80945e82ee93e5939baebdca47b9dee80a07d3144be1e1a6a66dd6a']
+
+dependencies = [
+    ('bzip2', '1.0.8'),
+    ('zlib', '1.2.13'),
+    ('XZ', '5.4.2'),
+    ('zstd', '1.5.5'),
+    ('ICU', '73.2'),
+]
+
+configopts = '--without-libraries=python,mpi'
+
+# disable MPI, build Boost libraries with tagged layout
+boost_mpi = False
+tagged_layout = True
+
+moduleclass = 'devel'

easybuild/easyconfigs/c/Cufflinks/Cufflinks-20190706-GCC-12.3.0.eb

@@ -0,0 +1,49 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+
+name = 'Cufflinks'
+version = '20190706'
+local_commit = 'dc3b0cb'
+
+homepage = 'http://cole-trapnell-lab.github.io/%(namelower)s/'
+description = "Transcript assembly, differential expression, and differential regulation for RNA-Seq"
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+toolchainopts = {'pic': True}
+
+github_account = 'cole-trapnell-lab'
+source_urls = [GITHUB_LOWER_SOURCE]
+sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}]
+patches = ['Cufflinks-20190706_fix-automake.patch']
+checksums = [
+    {'Cufflinks-20190706.tar.gz': '444c632083a473fe4fd99ff189cef5bbd95daee0912e8eefe79534bf225fbcb6'},
+    {'Cufflinks-20190706_fix-automake.patch': '4eb2eb9e8e549eb6c2e17493801c36554dbfb009d9af86e28195e898a350b3a6'},
+]
+
+builddependencies = [
+    ('Eigen', '3.4.0'),
+    ('Autotools', '20220317'),
+    ('SAMtools', '1.18'),
+    ('Boost', '1.75.0'),
+]
+
+dependencies = [
+    ('zlib', '1.2.13'),
+    ('HTSlib', '1.18'),
+]
+
+preconfigopts = 'autoreconf -i && export LIBS="${LIBS} -lhts" && export CFLAGS="$CFLAGS -fcommon" && '
+configopts = '--with-boost=${EBROOTBOOST} --with-bam=${EBROOTSAMTOOLS}'
+
+buildopts = "BOOST_FILESYSTEM_LIB=$EBROOTBOOST/lib/libboost_filesystem.a "
+buildopts += "BOOST_SERIALIZATION_LIB=$EBROOTBOOST/lib/libboost_serialization.a "
+buildopts += "BOOST_SYSTEM_LIB=$EBROOTBOOST/lib/libboost_system.a "
+buildopts += "BOOST_THREAD_LIB=$EBROOTBOOST/lib/libboost_thread.a "
+
+sanity_check_paths = {
+    'files': ['bin/cufflinks'],
+    'dirs': []
+}
+
+sanity_check_commands = ["cufflinks 2>&1 | grep 'Usage:.* cufflinks'"]
+
+moduleclass = 'bio'

easybuild/easyconfigs/c/Cufflinks/Cufflinks-20190706_fix-automake.patch

@@ -0,0 +1,14 @@
+fix for:
+error: AM_INIT_AUTOMAKE expanded multiple times
+author: Kenneth Hoste (HPC-UGent)
+--- cufflinks-dc3b0cb72a4ac2b6bbc887099e71fc0c21e107b7/configure.ac.orig	2019-07-06 18:28:01.000000000 +0200
++++ cufflinks-dc3b0cb72a4ac2b6bbc887099e71fc0c21e107b7/configure.ac	2024-09-27 13:39:13.512597490 +0200
+@@ -14,7 +14,7 @@
+ AC_CONFIG_SRCDIR([config.h.in])
+ AC_CONFIG_HEADERS([config.h])
+ AC_CONFIG_AUX_DIR([build-aux])
+-AM_INIT_AUTOMAKE
++#AM_INIT_AUTOMAKE
+
+ #AM_PATH_CPPUNIT(1.10.2)
+