From 40aaee4349775a552822d78ec57ca06a83d3bacc Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= <lukas.krupcik@vsb.cz>
Date: Thu, 25 Apr 2019 09:29:06 +0200
Subject: [PATCH] 	modified:   q/Qualimap/Qualimap-2.2.1.eb 
 modified:   r/R/R-3.5.3-intel-2017a.eb 	new file:  
 t/Trilinos/Trilinos-12.14.1-epetra_hdf5.patch 	modified:  
 t/Trilinos/Trilinos-12.14.1-intel-2017c-Py-2.7.eb

---
 q/Qualimap/Qualimap-2.2.1.eb                    |  5 +++--
 r/R/R-3.5.3-intel-2017a.eb                      | 17 +++++++++++++++++
 t/Trilinos/Trilinos-12.14.1-epetra_hdf5.patch   | 10 ++++++++++
 .../Trilinos-12.14.1-intel-2017c-Py-2.7.eb      |  9 +++++----
 4 files changed, 35 insertions(+), 6 deletions(-)
 create mode 100644 t/Trilinos/Trilinos-12.14.1-epetra_hdf5.patch

diff --git a/q/Qualimap/Qualimap-2.2.1.eb b/q/Qualimap/Qualimap-2.2.1.eb
index 812c87c2..e5ea829a 100644
--- a/q/Qualimap/Qualimap-2.2.1.eb
+++ b/q/Qualimap/Qualimap-2.2.1.eb
@@ -11,13 +11,14 @@ description = """Qualimap 2 is a platform-independent application written in
  interface to facilitate the quality control of alignment sequencing data and its
  derivatives like feature counts."""
 
-toolchain = {'name': 'dummy', 'version': ''}
+toolchain = {'name': 'intel', 'version': '2017a'}
 
 sources = ['qualimap_v2.2.1.zip']
 source_urls = ['https://bitbucket.org/kokonech/qualimap/downloads']
 
 dependencies = [
-    ('Java', '1.8.0_121'),
+    ('Java', '1.8.0_121', '', True),
+    ('R', '3.5.3'),
 ]
 
 cmds_map = [('.*', "./compile.sh")]
diff --git a/r/R/R-3.5.3-intel-2017a.eb b/r/R/R-3.5.3-intel-2017a.eb
index 3a0b5320..439f0aa2 100644
--- a/r/R/R-3.5.3-intel-2017a.eb
+++ b/r/R/R-3.5.3-intel-2017a.eb
@@ -2075,6 +2075,23 @@ exts_list = [
     ('BiocGenerics', '0.28.0'),
     ('Biobase', '2.42.0'),
     ('NOISeq', '2.26.1'),
+    ('S4Vectors', '0.20.1'),
+    ('IRanges', '2.16.0'),
+    ('GenomeInfoDbData', '1.2.0'),
+    ('GenomeInfoDb', '1.18.2'),
+    ('zlibbioc', '1.28.0'),
+    ('XVector', '0.22.0'),
+    ('GenomicRanges', '1.34.0'),
+    ('Biostrings', '2.50.2'),
+    ('BiocParallel', '1.16.6'),
+    ('Rsamtools', '1.34.1'),
+    ('DelayedArray', '0.8.0'),
+    ('SummarizedExperiment', '1.12.0'),
+    ('GenomicAlignments', '1.18.1'),
+    ('rtracklayer', '1.42.2'),
+    ('BSgenome', '1.50.0'),
+    ('gsmoothr', '0.1.7'),
+    ('limma', '3.14.4'),
 ]
 
 moduleclass = 'lang'
diff --git a/t/Trilinos/Trilinos-12.14.1-epetra_hdf5.patch b/t/Trilinos/Trilinos-12.14.1-epetra_hdf5.patch
new file mode 100644
index 00000000..34e779e9
--- /dev/null
+++ b/t/Trilinos/Trilinos-12.14.1-epetra_hdf5.patch
@@ -0,0 +1,10 @@
+--- packages/epetraext/test/inout/CMakeLists.txt.orig	2019-04-24 13:19:22.095883629 +0200
++++ packages/epetraext/test/inout/CMakeLists.txt	2019-04-24 13:19:36.249871114 +0200
+@@ -11,6 +11,7 @@
+ 
+ TRIBITS_ADD_EXECUTABLE_AND_TEST(
+   inout_hdf5_test
++  EXCLUDE_IF_NOT_TRUE ${PACKAGE_NAME}_ENABLE_HDF5
+   SOURCES
+     EpetraExt_HDF5_UnitTest.cpp
+   COMM serial mpi
diff --git a/t/Trilinos/Trilinos-12.14.1-intel-2017c-Py-2.7.eb b/t/Trilinos/Trilinos-12.14.1-intel-2017c-Py-2.7.eb
index a5bd8719..c55898bd 100644
--- a/t/Trilinos/Trilinos-12.14.1-intel-2017c-Py-2.7.eb
+++ b/t/Trilinos/Trilinos-12.14.1-intel-2017c-Py-2.7.eb
@@ -14,14 +14,15 @@ toolchainopts = {'usempi': True, 'pic': True, 'strict': True}
 
 source_urls = ['https://github.com/trilinos/Trilinos/archive/']
 sources = ['%(namelower)s-release-12-14-1.tar.gz']
-#patches = [
+patches = [
+     ('Trilinos-12.14.1-epetra_hdf5.patch'),
 #    ('Trilinos-12.12.1_fix-CEpetra-LAPACK.patch', 'packages/CTrilinos'),
 #    'Trilinos-12.12.1_muelu-fix-function-signature.patch',
 #    'Trilinos-12.12.1_fix-Sundance.patch',
-#]
+]
 
-#configopts = '-D EpetraExt_inout_hdf5_test_MPI_4_DISABLE=ON'
-configopts = '-DEpetraExt_ENABLE_HDF5=OFF'
+configopts =  '-DThyraEpetraAdapters_TestThyraDebugHang_MPI_4_DISABLE=ON '
+configopts += '-DEpetraExt_ENABLE_HDF5=OFF '
 
 builddependencies = [
     ('CMake', '3.13.1', '', True),