Merge branch 'it4i-salomon'

b/bcl2fastq2/\

@@ -1,39 +0,0 @@
-# IT4Innovations 2019
-
-easyblock = 'ConfigureMake'
-
-name = 'bcl2fastq2'
-version = '2.20.0'
-versionsuffix = '-Py-3.6'
-
-homepage = 'https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html'
-description = """bcl2fastq Conversion Software both demultiplexes data and converts BCL files generated by
- Illumina sequencing systems to standard FASTQ file formats for downstream analysis."""
-
-toolchain = {'name': 'intel', 'version': '2017a'}
-
-source_urls = [
-    'ftp://webdata2:webdata2@ussd-ftp.illumina.com/downloads/software/bcl2fastq/']
-sources = [{
-    'filename': '%(name)s-v2-20-0-tar.zip',
-    # source file is a .zip that contains a .tar.gz
-    'extract_cmd': 'unzip -p %s | tar -xzvf -',
-}]
-
-start_dir = 'src'
-configopts = '--force-builddir --with-cmake=cmake '
-
-builddependencies = [
-    ('CMake', '3.8.1', '', True),
-]
-
-dependencies = [
-    ('Py', '3.6', '', True),
-]
-
-sanity_check_paths = {
-    'files': ['bin/bcl2fastq'],
-    'dirs': ['lib']
-}
-
-moduleclass = 'bio'

q/Qt/Qt-4.8.7.eb

@@ -13,7 +13,7 @@ source_urls = [
 ]
 sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz']
 
-dependencies = [('GLib', '2.52.0')]
+dependencies = [('GLib', '2.57.1')]
 
 platform = 'linux-g++-64'
 

q/Qualimap/Qualimap-2.2.1-intel-2017a-Py-3.6.eb

@@ -0,0 +1,31 @@
+# IT4Innovations 2019
+
+easyblock = "Tarball"
+
+name = 'Qualimap'
+version = '2.2.1'
+versionsuffix = '-Py-3.6'
+
+homepage = 'http://qualimap.bioinfo.cipf.es/'
+description = """Qualimap 2 is a platform-independent application written in
+ Java and R that provides both a Graphical User Inteface (GUI) and a command-line
+ interface to facilitate the quality control of alignment sequencing data and its
+ derivatives like feature counts."""
+
+toolchain = {'name': 'intel', 'version': '2017a'}
+
+sources = ['qualimap_v%(version)s.zip']
+source_urls = ['https://bitbucket.org/kokonech/qualimap/downloads']
+
+dependencies = [
+    ('R', '3.5.3', '-Py-3.6'),
+]
+
+modextrapaths = {"PATH": '.'}
+
+sanity_check_paths = {
+    'files': ['qualimap'],
+    'dirs': ['lib', 'scripts', 'species'],
+}
+
+moduleclass = 'bio'