Merge pull request #14325 from sassy-crick/20211111132939_new_pr_Kent…

…_tools422 add patch for Kent_tools v422 to ensure OpenSSL dependency is used + add missing freetype dependency
easybuilders · Nov 11, 2021 · da84e09 · da84e09
2 parents 543218d + 719b03d
commit da84e09
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Showing 2 changed files with 54 additions and 4 deletions.
diff --git a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-422-GCC-11.2.0.eb b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-422-GCC-11.2.0.eb
@@ -12,23 +12,28 @@ source_urls = [
     'https://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/',
 ]
 sources = ['userApps.v%(version)s.src.tgz']
-checksums = ['1edf66ad5f7c8c79586e9f878b5971d7d467c8c5efbeb31c69085d24a6e4671f']
-
-files_to_copy = [(['bin/*'], 'bin'), 'licenseBlat.txt', 'licenseUcscGenomeBrowser.txt']
+patches = ['%(name)s-%(version)s-openssl.patch']
+checksums = [
+    '1edf66ad5f7c8c79586e9f878b5971d7d467c8c5efbeb31c69085d24a6e4671f',  # userApps.v422.src.tgz
+    'eedd328fc8a8e01806f4de9e8dce5b2a149edf493a17c3758803853e7881f240',  # Kent_tools-422-openssl.patch
+]
 
 dependencies = [
     ('MariaDB', '10.6.4'),
     ('libpng', '1.6.37'),
     ('zlib', '1.2.11'),
     ('util-linux', '2.37'),
     ('OpenSSL', '1.1', '', True),
+    ('freetype', '2.11.0'),
 ]
 
 buildopts = 'CC="$CC" COPT="$CFLAGS -fcommon" PNGLIB="-L$EBROOTLIBPNG/lib -lpng" ZLIB="-L$EBROOTZLIB/lib -lz" '
-buildopts += 'MYSQLLIBS="-L$EBROOTMARIADB/lib -lmariadb -lstdc++" '
+buildopts += 'SSL_DIR="$EBROOTOPENSSL" SSLDIR="$EBROOTOPENSSL" MYSQLLIBS="-L$EBROOTMARIADB/lib -lmariadb -lstdc++" '
 
 local_binaries = ['blat', 'bedPartition', 'getRna', 'liftOver', 'mafGene', 'splitFile', 'twoBitToFa']
 
+files_to_copy = [(['bin/*'], 'bin'), 'licenseBlat.txt', 'licenseUcscGenomeBrowser.txt']
+
 sanity_check_paths = {
     'files': ['bin/%s' % x for x in local_binaries],
     'dirs': [],

diff --git a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-422-openssl.patch b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-422-openssl.patch
@@ -0,0 +1,45 @@
+Patch to ensure SSL will be picked up by EasyBuild and not the OS. Important for older OpenSSL versions
+Author: J. Sassmannshausen / GSTT
+diff --git a/userApps.orig/kent/src/inc/common.mk b/userApps/kent/src/inc/common.mk
+index d200b43..cb257d6 100644
+--- a/userApps.orig/kent/src/inc/common.mk
++++ b/userApps/kent/src/inc/common.mk
+@@ -133,7 +133,7 @@ endif
+ ifneq (${SSL_DIR}, "/usr/include/openssl")
+   ifneq ($(UNAME_S),Darwin)
+     ifneq ($(wildcard ${SSL_DIR}),)
+-      L+=-L${SSL_DIR}/lib
++      L+=-L${SSL_DIR}/lib -lssl -lcrypto
+     endif
+   endif
+     HG_INC+=-I${SSL_DIR}/include
+@@ -142,29 +142,6 @@ endif
+ ifeq (${IS_HGWDEV},yes)
+    L+=/hive/groups/browser/freetype/freetype-2.10.0/objs/.libs/libfreetype.a -lbz2
+    L+=/usr/lib64/libssl.a /usr/lib64/libcrypto.a -lkrb5 -lk5crypto -ldl
+-else
+-   ifneq ($(wildcard /opt/local/lib/libssl.a),)
+-       L+=/opt/local/lib/libssl.a
+-   else
+-     ifneq ($(wildcard /usr/lib/x86_64-linux-gnu/libssl.a),)
+-	L+=/usr/lib/x86_64-linux-gnu/libssl.a
+-     else
+-        ifneq ($(wildcard /usr/local/opt/openssl/lib/libssl.a),)
+-           L+=/usr/local/opt/openssl/lib/libssl.a
+-        else
+-           L+=-lssl
+-        endif
+-     endif
+-   endif
+-   ifneq ($(wildcard /opt/local/lib/libcrypto.a),)
+-       L+=/opt/local/lib/libcrypto.a
+-   else
+-        ifneq ($(wildcard /usr/local/opt/openssl/lib/libcrypto.a),)
+-           L+=/usr/local/opt/openssl/lib/libcrypto.a
+-        else
+-           L+=-lcrypto
+-        endif
+-   endif
+ endif
+
+ # autodetect where libm is installed