{bio} [intel/2017a] Trinity 2.5.1

easybuild/easyconfigs/t/Trinity/Trinity-2.5.1-intel-2017a.eb

@@ -0,0 +1,41 @@
+name = 'Trinity'
+version = '2.5.1'
+
+homepage = 'http://trinityrnaseq.github.io'
+description = """Trinity represents a novel method for the efficient and robust de novo reconstruction
+ of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm,
+ Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads."""
+toolchain = {'name': 'intel', 'version': '2017a'}
+toolchainopts = {'optarch': True}
+preinstallopts = "JAVA_TOOL_OPTIONS=-Dfile.encoding=UTF8 "
+
+source_urls = ['https://github.com/trinityrnaseq/trinityrnaseq/archive/']
+sources = ['%(name)s-v%(version)s.tar.gz']
+patches = [
+    'chrysalis_commandline_noconsts_2012-10-05.patch',
+    'Trinity-2.5.1_plugins-Makefile.patch',
+    'Trinity-2.5.1_icpc.patch',
+]
+checksums = [
+    'bf14f96981bb028d7960dec895a1bcbda1fadbbe562a913b188559fd74b90457',  # Trinity-v2.5.1.tar.gz
+    # chrysalis_commandline_noconsts_2012-10-05.patch
+    '3442803c357576557de843c80b73436e59e9a99027d60f5f63bb3368eceb4a5c',
+    '2682f182264bf101d0a2b182ca4110f2d1ab16c56e69e804379023c1e1a48847',  # Trinity-2.5.1_plugins-Makefile.patch
+    'a686eafb11d063b8a604190389db98808aaedf3458973b4124c38c9019878901',  # Trinity-2.5.1_icpc.patch
+]
+
+builddependencies = [
+    ('Autotools', '20150215', '', ('GCCcore', '6.3.0')),
+]
+
+dependencies = [
+    ('Java', '1.8.0_121', '', True),
+    ('ant', '1.10.1', '-Java-%(javaver)s', True),
+    ('Bowtie', '1.1.2'),
+    ('Bowtie2', '2.3.2'),
+    ('ncurses', '6.0'),
+    ('zlib', '1.2.11'),
+    ('Perl', '5.24.1'),
+]
+
+moduleclass = 'bio'

easybuild/easyconfigs/t/Trinity/Trinity-2.5.1_icpc.patch

@@ -0,0 +1,80 @@
+do not use ambiguous "end"
+do not compare input file stream with integer
+author: Samuel Moors (Free University of Brussels)
+--- ./Chrysalis/GraphFromFasta_MPI.cc.orig	2017-11-21 15:10:35.915874040 +0100
++++ ./Chrysalis/GraphFromFasta_MPI.cc	2017-11-21 15:11:16.751868585 +0100
+@@ -49,7 +49,7 @@
+
+
+ #include<sys/time.h>
+-static struct timeval start,end;
++static struct timeval start,stop;
+ void timer_start(){
+
+   gettimeofday(&start,NULL);
+@@ -57,8 +57,8 @@
+
+
+ double timer_stop(){
+-  gettimeofday(&end,NULL);
+-  double time_taken = ((end.tv_usec-start.tv_usec) + 1000000*(end.tv_sec - start.tv_sec));
++  gettimeofday(&stop,NULL);
++  double time_taken = ((stop.tv_usec-start.tv_usec) + 1000000*(stop.tv_sec - start.tv_sec));
+  time_taken = time_taken/1000;
+   return time_taken;
+ }
+--- ./Chrysalis/ReadsToTranscripts_MPI_chang.cc.orig	2017-10-20 14:42:21.000000000 +0200
++++ ./Chrysalis/ReadsToTranscripts_MPI_chang.cc	2017-11-21 15:43:02.489700214 +0100
+@@ -34,7 +34,7 @@
+ }
+
+ #include<sys/time.h>
+-static struct timeval start,end;
++static struct timeval start,stop;
+ void timer_start(){
+
+   gettimeofday(&start,NULL);
+@@ -42,8 +42,8 @@
+
+
+ double timer_stop(){
+-  gettimeofday(&end,NULL);
+-  double time_taken = ((end.tv_usec-start.tv_usec) + 1000000*(end.tv_sec - start.tv_sec));
++  gettimeofday(&stop,NULL);
++  double time_taken = ((stop.tv_usec-start.tv_usec) + 1000000*(stop.tv_sec - start.tv_sec));
+  time_taken = time_taken/1000;
+   return time_taken;
+ }
+--- ./Chrysalis/ReadsToTranscripts_MPI.cc.orig	2017-10-20 14:42:21.000000000 +0200
++++ ./Chrysalis/ReadsToTranscripts_MPI.cc	2017-11-21 15:40:23.293798438 +0100
+@@ -38,7 +38,7 @@
+
+ #include<sys/time.h>                                                                                                                                                                                                                      
+
+-static struct timeval start,end;                                                                                                                                                                                                           
++static struct timeval start,stop;                                                                                                                                                                                                           
+
+ void timer_start(){                                                                                                                                                                                                                        
+
+@@ -53,8 +53,8 @@
+
+ double timer_stop(){                                                                                                                                                                                            
+
+-    gettimeofday(&end,NULL);                                                                                                                                                                                                               
+-    double time_taken = ((end.tv_usec-start.tv_usec) + 1000000*(end.tv_sec - start.tv_sec));                                                                                                                                               
++    gettimeofday(&stop,NULL);                                                                                                                                                                                                               
++    double time_taken = ((stop.tv_usec-start.tv_usec) + 1000000*(stop.tv_sec - start.tv_sec));                                                                                                                                               
+     time_taken = time_taken/1000;                                                                                                                                                                                                         
+     return time_taken;                                                                                                                                                                                                                     
+
+--- ./Chrysalis/analysis/sequenceUtil.cc.orig	2017-11-21 14:34:37.449436229 +0100
++++ ./Chrysalis/analysis/sequenceUtil.cc	2017-11-21 14:36:07.653477550 +0100
+@@ -50,7 +50,7 @@
+ string read_sequence_from_file (string filename) {
+
+   ifstream fileReader (filename.c_str());
+-  if (fileReader == 0) { // couldn't open file
++  if (!fileReader) { // couldn't open file
+ 	throw(stacktrace() + "\n\nCould not open " + filename + "\n");
+   }
+

easybuild/easyconfigs/t/Trinity/Trinity-2.5.1_plugins-Makefile.patch

@@ -0,0 +1,21 @@
+use EasyBuild-provided zlib, don't hardcode gcc/g++ for jellyfish plugin
+authors: B. Hajgato (Vrije Universiteit Brussel), Kenneth Hoste (HPC-UGent)
+--- trinityrnaseq-Trinity-v2.5.1/trinity-plugins/Makefile.orig	2017-11-22 14:21:14.473780000 +0100
++++ trinityrnaseq-Trinity-v2.5.1/trinity-plugins/Makefile	2017-11-22 14:29:21.276480000 +0100
+@@ -20,6 +20,7 @@
+ ifeq ($(OS),Darwin)
+ 	sed -i.bak s/-rdynamic//g samtools-1.3.1/Makefile
+ endif
++	sed -e 's/ -lz/ -L\$$\{EBROOTZLIB\}\/lib -lz/' -i samtools-1.3.1/Makefile
+ 	cd samtools-1.3.1 && $(MAKE)
+ 	mv samtools-1.3.1/samtools ./BIN/.
+
+@@ -30,7 +31,7 @@
+
+ jellyfish:
+ 	tar -zxvf ${JELLYFISH_CODE}.tar.gz && ln -sf ${JELLYFISH_CODE} tmp.jellyfish
+-	cd ./tmp.jellyfish/ && ./configure CC=gcc CXX=g++ --enable-static --disable-shared --prefix=`pwd` && $(MAKE) LDFLAGS="-lpthread -all-static" AM_CPPFLAGS="-Wall -Wnon-virtual-dtor -I"`pwd`"/include"
++	cd ./tmp.jellyfish/ && ./configure CC=$(CC) CXX=$(CXX) --enable-static --disable-shared --prefix=`pwd` && $(MAKE) LDFLAGS="-lpthread -all-static" AM_CPPFLAGS="-Wall -Wnon-virtual-dtor -I"`pwd`"/include"
+ 	mv tmp.jellyfish jellyfish
+
+