update source_urls for Velvet 1.2.10

[branfosj]

(created using eb --new-pr)

[boegel]

@branfosj Is there an actual difference in contents of the source tarball?
Should we retain the old checksum as valid?

[branfosj]

@branfosj Is there an actual difference in contents of the source tarball? Should we retain the old checksum as valid?

I do not have the old version to check with. We are having a filename change, so we would have to do something more complicated...

[branfosj]

Test report by @branfosj
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
bear-pg0105u03a.bear.cluster - Linux RHEL 8.6, x86_64, Intel(R) Xeon(R) Platinum 8360Y CPU @ 2.40GHz (icelake), Python 3.6.8
See https://gist.github.com/branfosj/06699978b252e98a69aae0d6a4b93132 for a full test report.

[branfosj]

@boegelbot please test @ jsc-zen2
EB_ARGS="Velvet-1.2.10-GCC-11.2.0-mt-kmer_191.eb"

[boegelbot]

@branfosj: Request for testing this PR well received on jsczen2l1.int.jsc-zen2.easybuild-test.cluster

PR test command 'EB_PR=18237 EB_ARGS="Velvet-1.2.10-GCC-11.2.0-mt-kmer_191.eb" /opt/software/slurm/bin/sbatch --mem-per-cpu=4000M --job-name test_PR_18237 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen2.sh' executed!

• exit code: 0
• output:

Submitted batch job 2922

Test results coming soon (I hope)...

- notification for comment with ID 1613564911 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

[boegelbot]

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
jsczen2c1.int.jsc-zen2.easybuild-test.cluster - Linux Rocky Linux 8.5, x86_64, AMD EPYC 7742 64-Core Processor (zen2), Python 3.6.8
See https://gist.github.com/boegelbot/b1548c63aa80b547bc1ded41acb7414f for a full test report.

[boegel]

Code is not exactly the same as old source tarball, but it looks like we don't have many options here...

 $ diff -ru velvet_1.2.10 velvet-1.2.10
diff -ru velvet_1.2.10/Makefile velvet-1.2.10/Makefile
--- velvet_1.2.10/Makefile	2013-10-17 18:03:39.000000000 +0200
+++ velvet-1.2.10/Makefile	2014-08-15 18:13:23.000000000 +0200
@@ -3,8 +3,8 @@
 DEBUG = -g
 LIBS = -lm
 OPT = -O3
-MAXKMERLENGTH=31
-CATEGORIES=2
+MAXKMERLENGTH?=31
+CATEGORIES?=2
 DEF = -D MAXKMERLENGTH=$(MAXKMERLENGTH) -D CATEGORIES=$(CATEGORIES)
 PDFLATEX_VERSION := $(shell pdflatex --version 2> /dev/null)

diff -ru velvet_1.2.10/src/correctedGraph.c velvet-1.2.10/src/correctedGraph.c
--- velvet_1.2.10/src/correctedGraph.c	2013-10-17 18:03:39.000000000 +0200
+++ velvet-1.2.10/src/correctedGraph.c	2014-08-15 18:13:23.000000000 +0200
@@ -2094,9 +2094,11 @@
 		if (isTerminal(slowMarker))
 			slowLength = finalLength;
 		else {
-			slowLength =
-			    slowToFastMapping[getPassageMarkerFinish
-					      (slowMarker) - 1];
+			if(getPassageMarkerFinish(slowMarker) != 0)
+				slowLength = slowToFastMapping[getPassageMarkerFinish(slowMarker) - 1];
+			else
+				slowLength = slowToFastMapping[0];
+
 			if (slowLength < slowConstraint)
 				slowLength = slowConstraint;
 		}
diff -ru velvet_1.2.10/src/graph.c velvet-1.2.10/src/graph.c
--- velvet_1.2.10/src/graph.c	2013-10-17 18:03:39.000000000 +0200
+++ velvet-1.2.10/src/graph.c	2014-08-15 18:13:23.000000000 +0200
@@ -906,7 +906,7 @@
 	twinDestination->length = newLength;
 }

-static void catDescriptors(Descriptor * descr, Coordinate destinationLength, Descriptor * copy, Coordinate sourceLength)
+static void catDescriptors(Descriptor * descr, Coordinate destinationLength, Descriptor * copy, Coordinate sourceLength)
 {
 	Coordinate index;
 	Nucleotide nucleotide;
@@ -917,7 +917,7 @@
 	}
 }

-static void reverseCatDescriptors(Descriptor * descr, Coordinate destinationLength, Descriptor * copy, Coordinate sourceLength, Coordinate totalLength)
+static void reverseCatDescriptors(Descriptor * descr, Coordinate destinationLength, Descriptor * copy, Coordinate sourceLength, Coordinate totalLength)
 {
 	Coordinate shift = totalLength - destinationLength - sourceLength;
 	Coordinate index;
@@ -2052,7 +2052,7 @@
 	short short_var;
 	char c;

-	if (file == NULL)
+	if (file == NULL)
 		exitErrorf(EXIT_FAILURE, true, "Could not open %s", filename);

 	velvetLog("Reading graph file %s\n", filename);
@@ -2204,9 +2204,9 @@
 				velvetLog
 				    ("ERROR: reading in graph - only %d items read for line '%s'",
 				     sCount, line);
-#ifdef DEBUG
+#ifdef DEBUG
 				abort();
-#endif
+#endif
 				exit(1);
 			}
 			newMarker =
@@ -2404,7 +2404,7 @@
 #endif
 				}
 			}
-
+
 			index++;
 		}

@@ -2506,7 +2506,7 @@
 		twin = node->twinNode;
 		twin->length = node->length;
 		twin->descriptor =
-			callocOrExit(arrayLength, Descriptor);
+			callocOrExit(arrayLength, Descriptor);

 		index = 0;
 		while ((c = getc(file)) != '\n') {
@@ -3145,9 +3145,13 @@
 	}

 	free(sourceArray);
-	graph->nodeReads[sourceID] = newArray;
 	graph->nodeReadCounts[sourceID] = newLength;

+	if(newLength > 0)
+		graph->nodeReads[sourceID] = newArray;
+	else
+		graph->nodeReads[sourceID] = NULL;
+
 	*length = mergeLength;
 	return mergeArray;
 }
@@ -3275,9 +3279,13 @@
 	}

 	free(sourceArray);
-	graph->nodeReads[sourceID] = newArray;
 	graph->nodeReadCounts[sourceID] = newLength;

+	if(newLength > 0)
+		graph->nodeReads[sourceID] = newArray;
+	else
+		graph->nodeReads[sourceID] = NULL;
+
 	*length = mergeLength;
 	return mergeArray;
 }
@@ -3321,8 +3329,13 @@
 			sourceIndex++;
 		}

-		graph->nodeReads[targetID] = mergeArray;
 		graph->nodeReadCounts[targetID] = sourceLength;
+
+		if(sourceLength > 0)
+		    graph->nodeReads[targetID] = mergeArray;
+		else
+		    graph->nodeReads[targetID] = NULL;
+
 		return;
 	}

@@ -3402,8 +3415,12 @@
 	}

 	free(targetArray);
-	graph->nodeReads[targetID] = mergeArray;
 	graph->nodeReadCounts[targetID] = mergeLength;
+
+	if(mergeLength > 0)
+		graph->nodeReads[targetID] = mergeArray;
+	else
+		graph->nodeReads[targetID] = NULL;
 }

 static inline Coordinate min(Coordinate A, Coordinate B)
@@ -3437,8 +3454,13 @@

 	if (targetLength == 0) {
 		free(targetArray);
-		graph->nodeReads[targetID] = sourceArray;
 		graph->nodeReadCounts[targetID] = sourceLength;
+
+		if(sourceLength > 0)
+			graph->nodeReads[targetID] = sourceArray;
+		else
+			graph->nodeReads[targetID] = NULL;
+
 		return;
 	}

@@ -3548,9 +3570,13 @@
 	}

 	free(targetArray);
-	graph->nodeReads[targetID] = mergeArray;
 	graph->nodeReadCounts[targetID] = mergeLength;

+	if(mergeLength > 0)
+		graph->nodeReads[targetID] = mergeArray;
+	else
+		graph->nodeReads[targetID] = NULL;
+
 	free(sourceArray);
 }

@@ -3693,12 +3719,20 @@
 	}

 	free(targetArray);
-	graph->nodeReads[targetID] = mergeArray;
 	graph->nodeReadCounts[targetID] = mergeLength;

+	if(mergeLength > 0)
+		graph->nodeReads[targetID] = mergeArray;
+	else
+		graph->nodeReads[targetID] = NULL;
+
 	free(sourceArray);
-	graph->nodeReads[sourceID] = mergeArray2;
 	graph->nodeReadCounts[sourceID] = mergeLength;
+
+	if(mergeLength > 0)
+		graph->nodeReads[sourceID] = mergeArray2;
+	else
+		graph->nodeReads[sourceID] = NULL;
 }

 void shareReadStarts(Node * target, Node * source, Graph * graph)
@@ -3973,7 +4007,7 @@
 		nucleotide = getNucleotideInDescriptor(twin->descriptor, index);
 		writeNucleotideInDescriptor(nucleotide, array, index + shift);
 	}
-
+
 	free(twin->descriptor);
 	twin->descriptor = array;
 }
diff -ru velvet_1.2.10/src/scaffold.h velvet-1.2.10/src/scaffold.h
--- velvet_1.2.10/src/scaffold.h	2013-10-17 18:03:39.000000000 +0200
+++ velvet-1.2.10/src/scaffold.h	2014-08-15 18:13:23.000000000 +0200
@@ -18,7 +18,7 @@
     Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA

 */
-#ifndef _SSCAFFOLD_H_
+#ifndef _SCAFFOLD_H_
 #define _SCAFFOLD_H_

 typedef struct connection_st Connection;

[boegel]

lgtm

[boegel]

Test report by @boegel
SUCCESS
Build succeeded for 3 out of 3 (3 easyconfigs in total)
node3169.skitty.os - Linux RHEL 8.6, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz (skylake_avx512), Python 3.6.8
See https://gist.github.com/boegel/50fb085d32b459a5d935ce9b197db9eb for a full test report.

[boegel]

Going in, thanks @branfosj!