From 1cef9f746967fcea2bbc8536aad1d9be2b74bf73 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Tue, 6 Feb 2024 13:40:52 +0100
Subject: [PATCH] #235 #271 #71 progress

---
 235_singleM/SRA-Toolkit-3.0.10-gompi-2023a.eb       |  3 ++-
 ...0-GCCcore-12.3.0.eb => mfqe-0.5.0-GCC-12.3.0.eb} |  2 +-
 271_phyluce/btllib-1.7.0-GCC-12.3.0.eb              |  2 +-
 ...other-jar.eb => GRASPsuite-2023.05.09-system.eb} | 13 ++++++-------
 ...GRASPsuite-2022.7.4-system.eb => GRASPsuite2.eb} |  0
 5 files changed, 10 insertions(+), 10 deletions(-)
 rename 235_singleM/{mfqe-0.5.0-GCCcore-12.3.0.eb => mfqe-0.5.0-GCC-12.3.0.eb} (99%)
 rename 71_GRASP_suite/{GRASPsuite-other-jar.eb => GRASPsuite-2023.05.09-system.eb} (59%)
 rename 71_GRASP_suite/{GRASPsuite-2022.7.4-system.eb => GRASPsuite2.eb} (100%)

diff --git a/235_singleM/SRA-Toolkit-3.0.10-gompi-2023a.eb b/235_singleM/SRA-Toolkit-3.0.10-gompi-2023a.eb
index cd62d542..8fd79191 100644
--- a/235_singleM/SRA-Toolkit-3.0.10-gompi-2023a.eb
+++ b/235_singleM/SRA-Toolkit-3.0.10-gompi-2023a.eb
@@ -43,7 +43,8 @@ configopts = '-DVDB_INCDIR="$EBROOTNCBIMINVDB/include" -DVDB_LIBDIR="$EBROOTNCBI
 configopts += '-DBUILD_TOOLS_LOADERS=ON -DBUILD_TOOLS_INTERNAL=ON'
 
 
-buildopts = ' && cd ngs && make'
+# buildopts = ' && cd ngs && make'
+prebuildopts = 'cd ngs && make && cd - && '
 
 _sra_bin = [
     'abi-dump', 'abi-load', 'align-info', 'bam-load', 'cache-mgr', 'cg-load', 'copycat', 'fasterq-dump', 'fastq-dump',
diff --git a/235_singleM/mfqe-0.5.0-GCCcore-12.3.0.eb b/235_singleM/mfqe-0.5.0-GCC-12.3.0.eb
similarity index 99%
rename from 235_singleM/mfqe-0.5.0-GCCcore-12.3.0.eb
rename to 235_singleM/mfqe-0.5.0-GCC-12.3.0.eb
index 4265a486..c6939863 100644
--- a/235_singleM/mfqe-0.5.0-GCCcore-12.3.0.eb
+++ b/235_singleM/mfqe-0.5.0-GCC-12.3.0.eb
@@ -6,7 +6,7 @@ version = '0.5.0'
 homepage = 'https://github.com/wwood/mfqe'
 description = 'extract one or more sets of reads from a FASTQ (or FASTA) file by specifying their read names.'
 
-toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
 
 source_urls = ['https://github.com/wwood/mfqe/archive/']
 sources = ['v%(version)s.tar.gz']
diff --git a/271_phyluce/btllib-1.7.0-GCC-12.3.0.eb b/271_phyluce/btllib-1.7.0-GCC-12.3.0.eb
index 5b6f0802..960f1b09 100644
--- a/271_phyluce/btllib-1.7.0-GCC-12.3.0.eb
+++ b/271_phyluce/btllib-1.7.0-GCC-12.3.0.eb
@@ -19,7 +19,7 @@ sources = [{
         'keep_git_dir': True,
     }
 }]
-checksums = ['62936bf7b136c1628736d5b69ba9b7f738417fa19802e4e5e36c2bf35e7aa9fa']
+checksums = [None]
 
 dependencies = [
     ('Python', '3.11.3'),
diff --git a/71_GRASP_suite/GRASPsuite-other-jar.eb b/71_GRASP_suite/GRASPsuite-2023.05.09-system.eb
similarity index 59%
rename from 71_GRASP_suite/GRASPsuite-other-jar.eb
rename to 71_GRASP_suite/GRASPsuite-2023.05.09-system.eb
index 7b4e1b77..48155351 100644
--- a/71_GRASP_suite/GRASPsuite-other-jar.eb
+++ b/71_GRASP_suite/GRASPsuite-2023.05.09-system.eb
@@ -1,8 +1,8 @@
 easyblock = 'JAR'
 
 name = 'GRASP-suite'
-version = '2022-10-14'
-local_commit = '04744b0'
+version = '2023-05-09'
+local_commit = '97cceec'
 versionsuffix = '-Java-%(javaver)s'
 
 homepage = 'https://github.com/bodenlab/GRASP-suite/'
@@ -11,15 +11,14 @@ description = """GRASP-suite is a collection of tools and tutorials to perform a
 analyse ancestral sequence reconstruction."""
 
 toolchain = SYSTEM
-# https://github.com/bodenlab/GRASP/blob/04744b0ea3d802645b73ab7e799145d306ee437c/src/main/resources/grasp-repo/com/asr/bnkit/1.0/bnkit-1.0.jar
-source_urls = ['https://github.com/bodenlab/GRASP/blob/%s/src/main/resources/grasp-repo/com/asr/bnkit/1.0/' % local_commit]
+
+source_urls = ['https://github.com/bodenlab/GRASP-suite/blob/%s/content/project/graspcmd/archive/' % local_commit]
 sources = [{
-    "download_filename": "bnkit-1.0.jar",
+    "download_filename": "bnkit.jar",
     "filename": "%(name)s-%(version)s.jar",
 }]
-checksums = ['3f6009d23c28c5ebfddbc4de5deac8afab42acb512676ae821e57f97850db243']
+checksums = ['abb38d9dc799d9ee7342eaf829a1b68a02ca18896378eae81faa6a75f4b1fb24']
 
-# source_urls = ['https://github.com/bodenlab/GRASP/raw/%s/src/main/resources/lib/' % local_commit]
 dependencies = [('Java', '17')]
 
 postinstallcmds = [
diff --git a/71_GRASP_suite/GRASPsuite-2022.7.4-system.eb b/71_GRASP_suite/GRASPsuite2.eb
similarity index 100%
rename from 71_GRASP_suite/GRASPsuite-2022.7.4-system.eb
rename to 71_GRASP_suite/GRASPsuite2.eb