{bio}[GCC/8.3.0,GCCcore/8.3.0,system/system] lDDT v1.2, PSIPRED v4.02, CSBLAST v2.2.3

easybuild/easyconfigs/c/csblast/csblast-2.2.3-GCCcore-8.3.0.eb

@@ -0,0 +1,37 @@
+easyblock = 'MakeCp'
+
+name = 'csblast'
+version = '2.2.3'
+
+homepage = 'https://github.com/soedinglab/csblast/'
+description = """Context-specific extension of BLAST that significantly improves sensitivity and alignment quality."""
+
+toolchain = {'name': 'GCCcore', 'version': '8.3.0'}
+
+github_account = 'soedinglab'
+sources = ['v%(version)s.tar.gz']
+source_urls = [GITHUB_SOURCE]
+checksums = ['3cf8dc251e85af6942552eae3d33e45a5a1c6d73c5e7f1a00ce26d6974c0d434']  # csblast-2.2.3.tar.gz
+
+builddependencies = [
+    ('binutils', '2.32'),
+]
+
+dependencies = [
+    ('sparsehash', '2.0.3'),
+]
+
+start_dir = 'src'
+
+build_cmd_targets = 'csblast csbuild'
+
+buildopts = 'FLAGS=-fpermissive'
+
+files_to_copy = ['bin', 'data', 'LICENSE', 'README_CSBLAST']
+
+sanity_check_paths = {
+    'files': ['bin/csblast', 'bin/csbuild', 'data/K4000.crf', 'data/K4000.lib'],
+    'dirs': ['bin', 'data'],
+}
+
+moduleclass = 'bio'

easybuild/easyconfigs/l/lddt/lddt-1.2.eb

@@ -0,0 +1,23 @@
+easyblock = 'Tarball'
+
+name = 'lddt'
+version = '1.2'
+
+homepage = 'https://openstructure.org'
+description = """The local Distance Difference Test (lDDT) is a superposition-free score which evaluates local distance
+differences in a model compared to a reference structure."""
+
+toolchain = SYSTEM
+
+source_urls = ['https://openstructure.org/static/']
+sources = ['%(name)s-linux.zip']
+checksums = ['3f4f72dc790f64431d29f7ff04353d3bbade8c8c12a487a1a99240a82fc4fcec']
+
+modextrapaths = {'PATH': ''}
+
+sanity_check_paths = {
+    'files': ['lddt', 'stereo_chemical_props.txt'],
+    'dirs': [],
+}
+
+moduleclass = 'bio'

easybuild/easyconfigs/p/psipred/psipred-4.02-GCC-8.3.0.eb

@@ -0,0 +1,32 @@
+easyblock = 'MakeCp'
+
+name = 'psipred'
+version = '4.02'
+
+homepage = 'http://bioinf.cs.ucl.ac.uk'
+description = 'Accurate protein secondary structure prediction'
+
+toolchain = {'name': 'GCC', 'version': '8.3.0'}
+
+sources = ['%(name)s.%(version)s.tar.gz']
+source_urls = ['http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/']
+
+patches = ['psipred-4.02_fix_segfault.patch']
+
+checksums = [
+    'b4009b6a5f8b76c6d60ac91c4a743512d844864cf015c492fb6d1dc0d092c467',  # psipred.4.02.tar.gz
+    'd9e52ecf43b04640ebd0693df37871659d598abaec7a2c66264e9a79ee1baa82',  # psipred-4.02_fix_segfault.patch
+]
+
+parallel = 1
+start_dir = 'src'
+build_cmd_targets = 'all install'  # install copies binaries to ../bin
+
+files_to_copy = ['bin', 'data', 'LICENSE']
+
+sanity_check_paths = {
+    'files': ['bin/chkparse', 'bin/psipass2', 'bin/psipred', 'bin/seq2mtx'],
+    'dirs': ['bin', 'data'],
+}
+
+moduleclass = 'bio'

easybuild/easyconfigs/p/psipred/psipred-4.02_fix_segfault.patch

@@ -0,0 +1,42 @@
+Fixes a segmentation fault for inputs with lines longer than 254 characters
+author: Christoph Siegert (Leipzig University)
+
+diff --git a/src/sspred_avpred.c b/src/sspred_avpred.c
+index a6af260..a68b653 100644
+--- a/src/sspred_avpred.c
++++ b/src/sspred_avpred.c
+@@ -44,6 +44,8 @@ int             seqlen;
+
+ char seq[MAXSEQLEN];
+
++char buf[4096];
++
+ enum aacodes
+ {
+     ALA, ARG, ASN, ASP, CYS,
+@@ -238,7 +240,6 @@ predict(int argc, char **argv)
+ int             getmtx(FILE *lfil)
+ {
+     int             aa, i, j, naa;
+-    char            buf[256], *p;
+
+     if (fscanf(lfil, "%d", &naa) != 1)
+ 	fail("Bad mtx file - no sequence length!");
+@@ -251,7 +252,7 @@ int             getmtx(FILE *lfil)
+
+     while (!feof(lfil))
+     {
+-	if (!fgets(buf, 65536, lfil))
++	if (!fgets(buf, sizeof(buf), lfil))
+ 	    fail("Bad mtx file!");
+ 	if (!strncmp(buf, "-32768 ", 7))
+ 	{
+@@ -262,7 +263,7 @@ int             getmtx(FILE *lfil)
+ 		aa = aanum(seq[j]);
+ 		if (aa < 20)
+ 		    profile[j][aa] += 0000;
+-		if (!fgets(buf, 65536, lfil))
++		if (!fgets(buf, sizeof(buf), lfil))
+ 		    break;
+ 	    }
+ 	}