update source_urls for Velvet 1.2.10 by branfosj · Pull Request #18237 · easybuilders/easybuild-easyconfigs

branfosj · 2023-06-29T17:09:36Z

(created using eb --new-pr)

boegel · 2023-06-29T17:13:07Z

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

branfosj · 2023-06-29T17:14:45Z

@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 · 2023-06-29T17:20:12Z

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 · 2023-06-29T17:24:11Z

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

boegelbot · 2023-06-29T17:27:10Z

@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)...

Details

- 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 · 2023-06-29T17:27:58Z

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 · 2023-06-29T19:17:32Z

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

Details

 $ 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 · 2023-06-29T19:21:44Z

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 · 2023-06-29T19:22:04Z

Going in, thanks @branfosj!

upate source_urls for Velvet

73518df

boegel added the bug fix label Jun 29, 2023

boegel added this to the next release (4.7.3?) milestone Jun 29, 2023

and the other Velvet easyconfigs

7c226ca

restore accidentally deleted checksum

ef69e5b

branfosj mentioned this pull request Jun 29, 2023

use patch to make ncbi-vdb 2.11.2 compatible with HDF5 1.12.2 #18236

Merged

boegel changed the title ~~upate source_urls for Velvet~~ upate source_urls for Velvet 1.2.10 Jun 29, 2023

boegel approved these changes Jun 29, 2023

View reviewed changes

boegel changed the title ~~upate source_urls for Velvet 1.2.10~~ update source_urls for Velvet 1.2.10 Jun 29, 2023

boegel merged commit 664c17b into easybuilders:develop Jun 29, 2023

boegel added the change label Jun 29, 2023

branfosj deleted the 20230629180927_new_pr_Velvet1210 branch June 29, 2023 19:24

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update source_urls for Velvet 1.2.10#18237

update source_urls for Velvet 1.2.10#18237
boegel merged 3 commits intoeasybuilders:developfrom
branfosj:20230629180927_new_pr_Velvet1210

branfosj commented Jun 29, 2023

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branfosj commented Jun 29, 2023 •

edited

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branfosj commented Jun 29, 2023

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branfosj commented Jun 29, 2023 •

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