Updated cellranger

Update R
Added vartrix
Updated zstd

easyconfigs/b/BUSCO/BUSCO-4.1.4-IGB-gcc-8.2.0-Python-3.7.2.eb

@@ -21,6 +21,7 @@ dependencies = [
  ('SEPP','4.3.10','-Python-%(pyver)s'),
  ('augustus','3.3.3'),
  ('HMMER','3.3.1'),
+ ('BBMap','38.94','-Java-1.8.0_201',True),
 
 
 ]

easyconfigs/b/BUSCO/BUSCO-5.1.2-IGB-gcc-8.2.0-Python-3.7.2.eb

@@ -22,6 +22,7 @@ dependencies = [
  ('augustus','3.3.3'),
  ('HMMER','3.3.1'),
  ('MetaEuk','4'),
+ ('BBMap','38.94','-Java-1.8.0_201',True),
  ('BUSCO-db','4','',True),
 
 

easyconfigs/b/BUSCO/BUSCO-5.3.2-IGB-gcc-8.2.0-Python-3.7.2.eb

@@ -23,6 +23,7 @@ dependencies = [
  ('HMMER','3.3.1'),
  ('MetaEuk','4'),
  ('GUSHR','20200928','-Java-1.8.0_201',True),
+ ('BBMap','38.94','-Java-1.8.0_201',True),
  ('BUSCO-db','4','',True), 
 ]
 

easyconfigs/b/BUSCO/BUSCO-5.4.4-IGB-gcc-8.2.0-Python-3.7.2.eb

@@ -24,7 +24,7 @@ dependencies = [
  ('MetaEuk','4'),
  ('GUSHR','20200928','-Java-1.8.0_201',True),
  ('BUSCO-db','4','',True),
-
+ ('BBMap','38.94','-Java-1.8.0_201',True), 
 ]
 
 

easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5-IGB-gcc-8.2.0-Python-3.7.2.eb

@@ -0,0 +1,62 @@
+easyblock = 'PythonPackage'
+
+name = 'BiG-SCAPE'
+version = '1.1.5'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'https://git.wageningenur.nl/medema-group/BiG-SCAPE'
+description = """BiG-SCAPE (Biosynthetic Gene Similarity Clustering and Prospecting Engine) is a software package, written in Python, that constructs sequence similarity networks of Biosynthetic Gene Clusters (BGCs) and groups them into Gene Cluster Families (GCFs)"""
+
+toolchain = {'name': 'IGB-gcc', 'version': '8.2.0'}
+
+sources = ['v%(version)s.tar.gz']
+source_urls = ['https:/medema-group/BiG-SCAPE/archive/refs/tags/']
+
+dependencies = [('Python','3.7.2'),
+ ('Biopython','1.79','-Python-%(pyver)s'),
+ ('FastTree','2.1.11'),
+ ('HMMER','3.3.1'),
+
+]
+
+exts_default_options = {
+ 'source_urls': [PYPI_SOURCE],
+ 'sanity_pip_check': True,
+ 'use_pip': True
+}
+
+exts_defaultclass = "PythonPackage"
+exts_list = [
+]
+
+exts_defaultclass = "PythonPackage"
+exts_list = []
+
+use_pip = True
+sanity_pip_check = True
+unpack_sources = False
+#use_pip_for_deps = True
+
+exts_filter = ('python -c "import %(ext_name)s"', "")
+
+options = {'modulename': False }
+
+
+keepsymlinks = True
+
+sanity_check_paths = {
+ 'files': ['bin/bigscape.py'],
+ 'dirs': [],
+}
+
+postinstallcmds = [
+ 'unzip -d %(installdir)s/lib/python%(pyshortver)s/site-packages/BiG-SCAPE/Annotated_MIBiG_reference/ %(installdir)s/lib/python%(pyshortver)s/site-packages/BiG-SCAPE/Annotated_MIBiG_reference/MIBiG_1.3_final.zip',
+ 'unzip -d %(installdir)s/lib/python%(pyshortver)s/site-packages/BiG-SCAPE/Annotated_MIBiG_reference/ %(installdir)s/lib/python%(pyshortver)s/site-packages/BiG-SCAPE/Annotated_MIBiG_reference/MIBiG_1.4_final.zip',
+ 'unzip -d %(installdir)s/lib/python%(pyshortver)s/site-packages/BiG-SCAPE/Annotated_MIBiG_reference/ %(installdir)s/lib/python%(pyshortver)s/site-packages/BiG-SCAPE/Annotated_MIBiG_reference/MIBiG_2.1_final.zip',
+ 'unzip -d %(installdir)s/lib/python%(pyshortver)s/site-packages/BiG-SCAPE/Annotated_MIBiG_reference/ %(installdir)s/lib/python%(pyshortver)s/site-packages/BiG-SCAPE/Annotated_MIBiG_reference/MIBiG_3.1_final.zip'
+]
+
+modextrapaths = {
+}
+
+moduleclass = 'bio'

easyconfigs/c/cellranger/cellranger-7.2.0.eb

@@ -0,0 +1,26 @@
+easyblock = 'Tarball'
+
+name = 'cellranger'
+version = '7.2.0'
+
+homepage = 'https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger'
+description = """Cell Ranger is a set of analysis pipelines that process Chromium single cell 3 RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis."""
+
+toolchain = SYSTEM
+
+sources = ['%(name)s-%(version)s.tar.gz']
+source_urls = ['']
+
+dependencies = [('bcl2fastq2','2.20','-IGB-gcc-8.2.0')
+]
+
+keepsymlinks = True
+
+sanity_check_paths = {
+ 'files': ['cellranger'],
+ 'dirs': [],
+}
+
+modextrapaths = {'PATH':''}
+
+moduleclass = 'bio'

easyconfigs/e/ExonOntology/ExonOntology-20171018-IGB-gcc-8.2.0-Perl-5.28.1.eb

@@ -0,0 +1,35 @@
+easyblock = 'Tarball'
+
+name = 'ExonOntology'
+version = '20171018'
+versionsuffix = '-Perl-%(perlver)s'
+local_commit = '8e98097c'
+
+homepage = 'https://gitlab.com/ExonOntology/ExonOntology'
+description = """This project consists of a set of scripts that are necessary to perform offline Exon Ontology analyses. Briefly, it can accept a list of genomic sequences as input that represent exons (or parts of exons). The algorithm then retrieves the protein features that are encoded by these DNA sequences."""
+
+toolchain = {'name': 'IGB-gcc', 'version': '8.2.0'}
+
+sources = ['%s.tar.gz' % local_commit]
+source_urls = ['https://gitlab.com/ExonOntology/ExonOntology/-/archive/']
+
+patches = ['ExonOntology-%(version)s.patch']
+
+dependencies = [
+ ('Perl','5.28.1'),
+ ('MariaDB','10.3.17'),
+]
+
+keepsymlinks = True
+
+sanity_check_paths = {
+ 'files': ['scripts/EXONT_annotateSequences.pl'],
+ 'dirs': [],
+}
+
+modextrapaths = {'PATH':'scripts'}
+
+postinstallcmds = ['chmod 775 %(installdir)s/scripts/EXONT_annotateSequences.pl',
+ 'chmod 775 %(installdir)s/scripts/runTest.sh'
+]
+moduleclass = 'bio'

easyconfigs/e/ExonOntology/ExonOntology-20171018.patch

@@ -0,0 +1,19 @@
+diff -ru ExonOntology-8e98097c-8e98097cb2d85f38c08a70e3cc9b2a11e3141a6a.original/scripts/EXONT_annotateSequences.pl ExonOntology-8e98097c-8e98097cb2d85f38c08a70e3cc9b2a11e3141a6a/scripts/EXONT_annotateSequences.pl
+--- ExonOntology-8e98097c-8e98097cb2d85f38c08a70e3cc9b2a11e3141a6a.original/scripts/EXONT_annotateSequences.pl 2023-11-08 15:57:30.719082000 -0600
++++ ExonOntology-8e98097c-8e98097cb2d85f38c08a70e3cc9b2a11e3141a6a/scripts/EXONT_annotateSequences.pl 2023-11-08 15:58:20.411613195 -0600
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl 
++#!/usr/bin/env perl 
+
+ # ============================================================================
+ #
+@@ -12,7 +12,8 @@
+ # ============================================================================
+ # LIBRARIES
+ # ============================================================================
+-use lib "./lib/";
++use FindBin qw($Bin);
++use lib $Bin . '/..//lib';
+ use strict;
+ use ExonOntologyLib;
+ use Getopt::Std;

easyconfigs/l/lz4/lz4-1.9.2-IGB-gcc-8.2.0.eb

@@ -0,0 +1,29 @@
+easyblock = 'ConfigureMake'
+
+name = 'lz4'
+version = '1.9.2'
+
+homepage = 'https://lz4.github.io/lz4/'
+description = """LZ4 is lossless compression algorithm, providing compression speed at 400 MB/s per core. 
+ It features an extremely fast decoder, with speed in multiple GB/s per core."""
+
+toolchain = {'name': 'IGB-gcc', 'version': '8.2.0'}
+
+github_account = '%(name)s'
+source_urls = [GITHUB_SOURCE]
+sources = ['v%(version)s.tar.gz']
+
+builddependencies = [('binutils', '2.32')]
+
+skipsteps = ['configure']
+
+installopts = "PREFIX=%(installdir)s"
+
+runtest = 'check'
+
+sanity_check_paths = {
+ 'files': ["bin/lz4", "lib/liblz4.%s" % SHLIB_EXT, "include/lz4.h"],
+ 'dirs': ["lib/pkgconfig"]
+}
+
+moduleclass = 'lib'

easyconfigs/m/MOODS/MOODS-1.9.4.1-IGB-gcc-8.2.0-Python-3.7.2.eb

@@ -0,0 +1,42 @@
+easyblock = 'PythonPackage'
+
+name = 'MOODS'
+version = '1.9.4.1'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'https://www.cs.helsinki.fi/group/pssmfind/'
+description = """MOODS is a suite of algorithms for matching position weight matrices (PWM) against DNA sequences. It features advanced matrix matching algorithms implemented in C++ that can be used to scan hundreds of matrices against chromosome-sized sequences in few seconds."""
+
+toolchain = {'name': 'IGB-gcc', 'version': '8.2.0'}
+
+sources = ['MOODS-python-%(version)s.tar.gz']
+source_urls = ['https://pypi.python.org/packages/source/m/MOODS-python']
+
+dependencies = [
+ ('Python', '3.7.2'),
+]
+
+
+exts_default_options = {
+ 'source_urls': [PYPI_SOURCE],
+ 'sanity_pip_check': True,
+}
+
+exts_defaultclass = "PythonPackage"
+exts_list = []
+
+use_pip = True
+sanity_pip_check = True
+unpack_sources = False
+#use_pip_for_deps = True
+
+exts_filter = ('python -c "import %(ext_name)s"', "")
+
+options = {'modulename': 'MOODS' }
+
+sanity_check_paths = {
+ 'files': ['bin/moods-dna.py'],
+ 'dirs': ['lib/python%(pyshortver)s/site-packages/MOODS'],
+}
+
+moduleclass = 'bio'