add missing dependencies and add patch for fix incorrect ids for BRAKER v2.1.6

easybuild/easyconfigs/b/BRAKER/BRAKER-2.1.6-foss-2022a.eb

@@ -12,7 +12,11 @@ toolchain = {'name': 'foss', 'version': '2022a'}
 
 source_urls = ['https://github.com/Gaius-Augustus/BRAKER/archive/']
 sources = ['v%(version)s.tar.gz']
-checksums = ['eef3c4037364472988a010322cbd79b5171158f9c016f4383809adade4866c06']
+patches = ['BRAKER-%(version)s_fix-incorrect-ids.patch']
+checksums = [
+    {'v2.1.6.tar.gz': 'eef3c4037364472988a010322cbd79b5171158f9c016f4383809adade4866c06'},
+    {'BRAKER-2.1.6_fix-incorrect-ids.patch': '2b219de070d109637a2660a456a1f9ced48c58197385e3b3924ae90c84b41d41'},
+]
 
 dependencies = [
     ('Perl', '5.34.1'),
@@ -25,6 +29,8 @@ dependencies = [
     ('Exonerate', '2.4.0'),
     ('BLAST+', '2.13.0'),
     ('Biopython', '1.79'),
+    ('DIAMOND', '2.1.0'),
+    ('CDBtools', '0.99'),
 ]
 
 fix_perl_shebang_for = ['scripts/*.pl']

easybuild/easyconfigs/b/BRAKER/BRAKER-2.1.6_fix-incorrect-ids.patch

@@ -0,0 +1,44 @@
+From f38630c1cad3e11b525f84d517c7949cb4c2d7eb Mon Sep 17 00:00:00 2001
+From: Katharina Hoff <katharina.hoff@gmail.com>
+Date: Mon, 19 Apr 2021 16:34:57 +0200
+Subject: [PATCH] fixing part of the issue
+ https://github.com/Gaius-Augustus/BRAKER/issues/354 where gene and transcript
+ line have incorrect ids
+
+---
+ scripts/merge_transcript_sets.pl | 8 ++++----
+ 1 file changed, 4 insertions(+), 4 deletions(-)
+
+diff --git a/scripts/merge_transcript_sets.pl b/scripts/merge_transcript_sets.pl
+index 04f6c3e..5cfd6c0 100755
+--- a/scripts/merge_transcript_sets.pl
++++ b/scripts/merge_transcript_sets.pl
+@@ -83,14 +83,15 @@
+             my $txid;
+             if($line =~ m/transcript_id/){
+                 $line =~ m/transcript_id "([^"]+)";/;
++
+                 $txid = $1;
+                 push(@{$txid_to_elements{$txid}}, $line);
+                 foreach(@store_for_txid){
+-                    push(@{$txid_to_elements{$txid}}, $_)
++                    push(@{$txid_to_elements{$txid}}, $_);
+                 }
+                 @store_for_txid = ();
+             }else{
+-                $line =~ s/\t([\t]+)$/\tfile_${file_counter}_$1/;
++                $line =~ s/\t([^\t]+)$/\tfile_${file_counter}_$1/;
+                 push(@store_for_txid, $line);
+             }
+             # currently, UTR features are ignored
+@@ -111,9 +112,8 @@
+     # always keep the first occuring transcript structure, only add from other gene sets if it has not been in the set, yet
+     # this might discard alternative UTR splicing isoforms at present
+     while (my ($key, $value) = each (%txid_to_struct_local)){
+-        #print "key is $key and value is $value\n";
++        print "key is $key and value is $value\n";
+         if(not(defined($uniq_struct_to_txid{$value}))){
+-            #print "adding transcript\n";
+             $uniq_struct_to_txid{$value} = $key;
+         }
+     }

easybuild/easyconfigs/c/CDBtools/CDBtools-0.99-GCC-11.3.0.eb

@@ -0,0 +1,29 @@
+easyblock = 'MakeCp'
+
+name = 'CDBtools'
+version = '0.99'
+
+homepage = 'http://compbio.dfci.harvard.edu/tgi'
+description = "CDB (Constant DataBase) indexing and retrieval tools for FASTA files"
+
+toolchain = {'name': 'GCC', 'version': '11.3.0'}
+
+source_urls = ['ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/cdbfasta']
+sources = [{'download_filename': 'cdbfasta.tar.gz', 'filename': SOURCE_TAR_GZ}]
+checksums = ['68767e8b2fb9de5a6d68ee16df73293f65e02f05cf2f747a9dd6b8854766722c']
+
+buildopts = 'CC="$CXX" DBGFLAGS="$CXXFLAGS"'
+
+files_to_copy = [(['cdbfasta', 'cdbyank'], 'bin')]
+
+sanity_check_paths = {
+    'files': ['bin/cdbfasta', 'bin/cdbyank'],
+    'dirs': [],
+}
+
+sanity_check_commands = [
+    "cdbfasta -v",
+    "cdbyank -v",
+]
+
+moduleclass = 'bio'