[med-svn] [Git][med-team/canu][master] 4 commits: Refreshed patches.
Michael R. Crusoe (@crusoe)
gitlab at salsa.debian.org
Thu Sep 4 12:38:23 BST 2025
Michael R. Crusoe pushed to branch master at Debian Med / canu
Commits:
60ee53cc by Michael R. Crusoe at 2025-09-04T12:49:03+02:00
Refreshed patches.
- - - - -
3164c700 by Michael R. Crusoe at 2025-09-04T12:49:03+02:00
Standards-Version: 4.7.2 (routine-update)
- - - - -
97b5b6d3 by Michael R. Crusoe at 2025-09-04T12:49:03+02:00
d/control: new build-deps zlib1g-dev, libcurl4-openssl-dev, liblzma-dev, libbz2-dev
- - - - -
e8020890 by Michael R. Crusoe at 2025-09-04T13:23:21+02:00
Add gnu-which & samtools to the dependencies
- - - - -
9 changed files:
- debian/changelog
- debian/control
- − debian/patches/cpuid
- − debian/patches/external-mhap.patch
- debian/patches/libsnappy
- debian/patches/series
- debian/patches/spelling
- debian/patches/stacktrace
- debian/patches/use-debian-mhap-at-runtime.patch
Changes:
=====================================
debian/changelog
=====================================
@@ -4,6 +4,11 @@ canu (2.3+dfsg-1) UNRELEASED; urgency=medium
* Team upload.
* d/control: simplify architecture specification using "architecture-
is-64-bit" and still allow x32.
+ * Refreshed patches.
+ * Standards-Version: 4.7.2 (routine-update)
+ * d/control: new build-deps: zlib1g-dev, libcurl4-openssl-dev, liblzma-dev,
+ libbz2-dev
+ new runtime-deps: samtools, gnu-which
[ Andreas Tille ]
* New upstream version
=====================================
debian/control
=====================================
@@ -10,8 +10,12 @@ Build-Depends: debhelper-compat (= 13),
# For File::Path
libfilesys-df-perl,
mhap,
+ zlib1g-dev,
+ libcurl4-openssl-dev,
+ liblzma-dev,
+ libbz2-dev,
debhelper
-Standards-Version: 4.7.0
+Standards-Version: 4.7.2
Vcs-Browser: https://salsa.debian.org/med-team/canu
Vcs-Git: https://salsa.debian.org/med-team/canu.git
Homepage: https://canu.readthedocs.org/en/latest/
@@ -24,6 +28,8 @@ Depends: ${shlibs:Depends},
${perl:Depends},
libfilesys-df-perl,
mhap,
+ gnu-which,
+ samtools,
gnuplot-nox | gnuplot
Suggests: nanopolish
Description: single molecule sequence assembler for genomes
=====================================
debian/patches/cpuid deleted
=====================================
@@ -1,206 +0,0 @@
-From: Michael R. Crusoe <crusoe at debian.org>
-Subject: enable cpuid on arm64, pcc64el, and other architectures
-Forwarded: https://github.com/jeffdaily/parasail/pull/102
-
---- canu.orig/src/utility/src/parasail/cpuid.c
-+++ canu/src/utility/src/parasail/cpuid.c
-@@ -13,6 +13,44 @@
-
- #include "parasail/cpuid.h"
-
-+#if defined(__arm__) || defined(__aarch64__) || defined(__powerpc__) || defined(__PPC__) || defined(__powerpc64__) || defined(__PPC64__)
-+
-+/* stubs for all non-x86_64 platforms */
-+int parasail_can_use_avx512vbmi() { return 0; }
-+int parasail_can_use_avx512bw() { return 0; }
-+int parasail_can_use_avx512f() { return 0; }
-+int parasail_can_use_avx2() { return 0; }
-+int parasail_can_use_sse41() { return 0; }
-+int parasail_can_use_sse2() { return 0; }
-+
-+#if defined(__powerpc__) || defined(__PPC__) || defined(__powerpc64__) || defined(__PPC64__)
-+int parasail_can_use_altivec()
-+{
-+#if HAVE_ALTIVEC
-+ return 1;
-+#else
-+ return 0;
-+#endif
-+}
-+#else
-+int parasail_can_use_altivec() { return 0; }
-+#endif
-+
-+#if defined(__arm__) || defined(__aarch64__)
-+int parasail_can_use_neon()
-+{
-+#if HAVE_NEON
-+ return 1;
-+#else
-+ return 0;
-+#endif
-+}
-+#else
-+int parasail_can_use_neon() { return 0; }
-+#endif
-+
-+#elif defined(__x86_64__) || defined(__i386__)
-+
- #include <stdint.h>
- #if defined(_MSC_VER)
- # include <intrin.h>
-@@ -33,7 +71,7 @@
- "+a" (eax), "+c" (ecx), "=d" (edx) );
- abcd[0] = eax; abcd[1] = ebx; abcd[2] = ecx; abcd[3] = edx;
- #endif
--}
-+}
-
-
- #if defined(__INTEL_COMPILER) && (__INTEL_COMPILER >= 1300)
-@@ -42,8 +80,13 @@
-
- static int check_4th_gen_intel_core_features()
- {
-- const int the_4th_gen_features =
-+ /* we only care about avx2, not the other features */
-+#if 0
-+ const int the_4th_gen_features =
- (_FEATURE_AVX2 | _FEATURE_FMA | _FEATURE_BMI | _FEATURE_LZCNT | _FEATURE_MOVBE);
-+#else
-+ const int the_4th_gen_features = _FEATURE_AVX2;
-+#endif
- return _may_i_use_cpu_feature( the_4th_gen_features );
- }
-
-@@ -69,7 +112,7 @@
-
- #else /* non-Intel compiler */
-
--static int check_xcr0_ymm()
-+static int check_xcr0_ymm()
- {
- #if HAVE_XGETBV
- uint32_t xcr0;
-@@ -102,31 +145,42 @@
-
- static int check_4th_gen_intel_core_features()
- {
-+ /* we only care about avx2, not the other features */
- uint32_t abcd[4];
-- uint32_t fma_movbe_osxsave_mask = ((1U << 12) | (1U << 22) | (1U << 27));
-- uint32_t avx2_bmi12_mask = (1U << 5) | (1U << 3) | (1U << 8);
--
-- /* CPUID.(EAX=01H, ECX=0H):ECX.FMA[bit 12]==1 &&
-- CPUID.(EAX=01H, ECX=0H):ECX.MOVBE[bit 22]==1 &&
-+ //uint32_t fma_movbe_osxsave_mask = ((1U << 12) | (1U << 22) | (1U << 27));
-+ //uint32_t avx2_bmi12_mask = (1U << 5) | (1U << 3) | (1U << 8);
-+ uint32_t avx2_mask = (1U << 5);
-+
-+#if 0
-+ /* CPUID.(EAX=01H, ECX=0H):ECX.FMA[bit 12]==1 &&
-+ CPUID.(EAX=01H, ECX=0H):ECX.MOVBE[bit 22]==1 &&
- CPUID.(EAX=01H, ECX=0H):ECX.OSXSAVE[bit 27]==1 */
- run_cpuid( 1, 0, abcd );
-- if ( (abcd[2] & fma_movbe_osxsave_mask) != fma_movbe_osxsave_mask )
-+ if ( (abcd[2] & fma_movbe_osxsave_mask) != fma_movbe_osxsave_mask )
- return 0;
-
- if ( ! check_xcr0_ymm() )
- return 0;
-+#endif
-
- /* CPUID.(EAX=07H, ECX=0H):EBX.AVX2[bit 5]==1 &&
- CPUID.(EAX=07H, ECX=0H):EBX.BMI1[bit 3]==1 &&
- CPUID.(EAX=07H, ECX=0H):EBX.BMI2[bit 8]==1 */
- run_cpuid( 7, 0, abcd );
-- if ( (abcd[1] & avx2_bmi12_mask) != avx2_bmi12_mask )
-+#if 0
-+ if ( (abcd[1] & avx2_bmi12_mask) != avx2_bmi12_mask )
- return 0;
-+#else
-+ if ( (abcd[1] & avx2_mask) != avx2_mask )
-+ return 0;
-+#endif
-
-+#if 0
- /* CPUID.(EAX=80000001H):ECX.LZCNT[bit 5]==1 */
- run_cpuid( 0x80000001, 0, abcd );
- if ( (abcd[2] & (1U << 5)) == 0)
- return 0;
-+#endif
-
- return 1;
- }
-@@ -141,7 +195,7 @@
-
- /* CPUID.(EAX=01H, ECX=0H):ECX.OSXSAVE[bit 27]==1 */
- run_cpuid( 1, 0, abcd );
-- if ( (abcd[2] & osxsave_mask) != osxsave_mask )
-+ if ( (abcd[2] & osxsave_mask) != osxsave_mask )
- return 0;
-
- if ( ! check_xcr0_zmm() )
-@@ -152,7 +206,7 @@
- CPUID.(EAX=07H, ECX=0H):EBX.AVX-512ER[bit 27]==1 &&
- CPUID.(EAX=07H, ECX=0H):EBX.AVX-512CD[bit 28]==1 */
- run_cpuid( 7, 0, abcd );
-- if ( (abcd[1] & avx512f_mask) != avx512f_mask )
-+ if ( (abcd[1] & avx512f_mask) != avx512f_mask )
- return 0;
-
- return 1;
-@@ -167,7 +221,7 @@
-
- /* CPUID.(EAX=01H, ECX=0H):ECX.OSXSAVE[bit 27]==1 */
- run_cpuid( 1, 0, abcd );
-- if ( (abcd[2] & osxsave_mask) != osxsave_mask )
-+ if ( (abcd[2] & osxsave_mask) != osxsave_mask )
- return 0;
-
- if ( ! check_xcr0_zmm() )
-@@ -177,7 +231,7 @@
- CPUID.(EAX=07H, ECX=0H):EBX.AVX-512DQ[bit 17]==1 &&
- CPUID.(EAX=07H, ECX=0H):EBX.AVX-512VL[bit 31]==1 */
- run_cpuid( 7, 0, abcd );
-- if ( (abcd[1] & avx512bw_mask) != avx512bw_mask )
-+ if ( (abcd[1] & avx512bw_mask) != avx512bw_mask )
- return 0;
-
- return 1;
-@@ -191,7 +245,7 @@
-
- /* CPUID.(EAX=01H, ECX=0H):ECX.OSXSAVE[bit 27]==1 */
- run_cpuid( 1, 0, abcd );
-- if ( (abcd[2] & osxsave_mask) != osxsave_mask )
-+ if ( (abcd[2] & osxsave_mask) != osxsave_mask )
- return 0;
-
- if ( ! check_xcr0_zmm() )
-@@ -199,7 +253,7 @@
-
- /* CPUID.(EAX=07H, ECX=0H):ECX.AVX-512VBMI[bit 1]==1 */
- run_cpuid( 7, 0, abcd );
-- if ( (abcd[2] & avx512vbmi_mask) != avx512vbmi_mask )
-+ if ( (abcd[2] & avx512vbmi_mask) != avx512vbmi_mask )
- return 0;
-
- return 1;
-@@ -311,3 +365,17 @@
- return 0;
- }
-
-+#else
-+
-+/* non-x86, non-ARM, non-PPC */
-+
-+int parasail_can_use_avx512vbmi() { return 0; }
-+int parasail_can_use_avx512bw() { return 0; }
-+int parasail_can_use_avx512f() { return 0; }
-+int parasail_can_use_avx2() { return 0; }
-+int parasail_can_use_sse41() { return 0; }
-+int parasail_can_use_sse2() { return 0; }
-+int parasail_can_use_altivec() { return 0; }
-+int parasail_can_use_neon() { return 0; }
-+
-+#endif
=====================================
debian/patches/external-mhap.patch deleted
=====================================
@@ -1,5 +0,0 @@
-Description: don't expect bundled MHAP
- the jar file has been removd from the Debian source.
-Author: Afif Elghraoui <afif at debian.org>
-Forwarded: not-needed
-Last-Update: 2018-03-10
=====================================
debian/patches/libsnappy
=====================================
@@ -2,9 +2,9 @@ Author: Michael R. Crusoe <crusoe at debian.org>
Description: use system package for snappy
Forwarded: not-needed
---- a/src/main.mk
-+++ b/src/main.mk
-@@ -105,10 +105,6 @@ SOURCES := utility/src/align/align-
+--- canu.orig/src/main.mk
++++ canu/src/main.mk
+@@ -105,10 +105,6 @@
stores/tgTigSizeAnalysis.C \
stores/tgTigMultiAlignDisplay.C \
\
@@ -15,43 +15,12 @@ Forwarded: not-needed
stores/objectStore.C \
\
overlapInCore/overlapReadCache.C \
---- a/src/Makefile
-+++ b/src/Makefile
-@@ -229,6 +229,7 @@ ifeq (${CANU_BUILD_ENV}, ports)
- CXXFLAGS += -pthread -fopenmp -fPIC
- CFLAGS += -pthread -fopenmp -fPIC
- LDFLAGS += -pthread -fopenmp -lm
-+ LDLIBS += -lsnappy
- else
- CC ?= cc
- CXX ?= c++
---- a/src/meryl/src/Makefile
-+++ b/src/meryl/src/Makefile
-@@ -229,6 +229,7 @@ ifeq (${CANU_BUILD_ENV}, ports)
- CXXFLAGS += -pthread -fopenmp -fPIC
- CFLAGS += -pthread -fopenmp -fPIC
- LDFLAGS += -pthread -fopenmp -lm
-+ LDLIBS += -lsnappy
- else
- CC ?= cc
- CXX ?= c++
---- a/src/seqrequester/src/Makefile
-+++ b/src/seqrequester/src/Makefile
-@@ -229,6 +229,7 @@ ifeq (${CANU_BUILD_ENV}, ports)
- CXXFLAGS += -pthread -fopenmp -fPIC
- CFLAGS += -pthread -fopenmp -fPIC
- LDFLAGS += -pthread -fopenmp -lm
-+ LDLIBS += -lsnappy
- else
- CC ?= cc
- CXX ?= c++
---- a/src/utility/src/Makefile
-+++ b/src/utility/src/Makefile
-@@ -229,6 +229,7 @@ ifeq (${CANU_BUILD_ENV}, ports)
- CXXFLAGS += -pthread -fopenmp -fPIC
- CFLAGS += -pthread -fopenmp -fPIC
- LDFLAGS += -pthread -fopenmp -lm
-+ LDLIBS += -lsnappy
- else
- CC ?= cc
- CXX ?= c++
+@@ -198,7 +194,7 @@
+
+ SYS_INCDIRS += $(shell pkg-config --cflags-only-I openssl libcurl liblzma | sed s:-I/:/:g)
+ LDFLAGS += $(shell pkg-config --libs-only-L openssl libcurl liblzma)
+-LDLIBS += $(shell pkg-config --libs-only-l openssl libcurl liblzma) -lz -lbz2
++LDLIBS += $(shell pkg-config --libs-only-l openssl libcurl liblzma) -lz -lbz2 -lsnappy
+
+ SUBMAKEFILES := stores/dumpBlob.mk \
+ stores/ovStoreBuild.mk \
=====================================
debian/patches/series
=====================================
@@ -1,6 +1,4 @@
use-debian-mhap-at-runtime.patch
-external-mhap.patch
libsnappy
stacktrace
spelling
-cpuid
=====================================
debian/patches/spelling
=====================================
@@ -2,86 +2,9 @@ From: Michael R. Crusoe <crusoe at debian.org>
Subject: typo fixes
Forwarded: https://github.com/marbl/canu/pull/2252
---- canu.orig/src/bogart/bogart.C
-+++ canu/src/bogart/bogart.C
-@@ -404,7 +404,7 @@
- fprintf(stderr, " -cp P Split a contig if there is an alternate path from an overlap at most P percent\n");
- fprintf(stderr, " different from the length of the best overlap. Default: 200.\n");
- fprintf(stderr, "\n");
-- fprintf(stderr, " -dg D Use overlaps upto D standard deviations from the mean when building the best\n");
-+ fprintf(stderr, " -dg D Use overlaps up to D standard deviations from the mean when building the best\n");
- fprintf(stderr, " overlap graph. Default 6.0.\n");
- fprintf(stderr, " -db D Like -dg, but for merging bubbles into primary contigs. Default 6.0.\n");
- fprintf(stderr, " -dr D Like -dg, but for breaking repeats. Default 3.0.\n");
---- canu.orig/src/gfa/alignGFA.C
-+++ canu/src/gfa/alignGFA.C
-@@ -655,7 +655,7 @@
- delete seqsp;
- delete gfa;
-
-- fprintf(stderr, "-- Aligned %6u ciruclar tigs, failed %6u\n", passCircular, failCircular);
-+ fprintf(stderr, "-- Aligned %6u circular tigs, failed %6u\n", passCircular, failCircular);
- fprintf(stderr, "-- Aligned %6u linear tigs, failed %6u\n", passNormal, failNormal);
- }
-
---- canu.orig/src/gfa/gfa.C
-+++ canu/src/gfa/gfa.C
-@@ -321,7 +321,7 @@
- char type = L[0];
-
- if (L[1] != '\t')
-- fprintf(stderr, "gfaFile::loadFile()-- misformed file; second letter must be tab in line '%s'\n", L), exit(1);
-+ fprintf(stderr, "gfaFile::loadFile()-- malformed file; second letter must be tab in line '%s'\n", L), exit(1);
-
- if (type == 'H') {
- delete [] _header;
---- canu.orig/src/overlapBasedTrimming/splitReads.C
-+++ canu/src/overlapBasedTrimming/splitReads.C
-@@ -159,7 +159,7 @@
- fprintf(stderr, " -t bgn-end limit processing to only reads from bgn to end (inclusive)\n");
- fprintf(stderr, "\n");
- fprintf(stderr, " -Ci clearFile path to input clear ranges\n");
-- fprintf(stderr, " -Co clearFile path to ouput clear ranges\n");
-+ fprintf(stderr, " -Co clearFile path to output clear ranges\n");
- fprintf(stderr, "\n");
- fprintf(stderr, " -e erate ignore overlaps with more than 'erate' percent error\n");
- //fprintf(stderr, " -l length ignore overlaps shorter than 'l' aligned bases (NOT SUPPORTED)\n");
---- canu.orig/src/overlapBasedTrimming/trimReads.C
-+++ canu/src/overlapBasedTrimming/trimReads.C
-@@ -191,7 +191,7 @@
- fprintf(stderr, "\n");
- fprintf(stderr, " -Ci clearFile path to input clear ranges (NOT SUPPORTED)\n");
- //fprintf(stderr, " -Cm clearFile path to maximal clear ranges\n");
-- fprintf(stderr, " -Co clearFile path to ouput clear ranges\n");
-+ fprintf(stderr, " -Co clearFile path to output clear ranges\n");
- fprintf(stderr, "\n");
- fprintf(stderr, " -e erate ignore overlaps with more than 'erate' percent error\n");
- //fprintf(stderr, " -l length ignore overlaps shorter than 'l' aligned bases (NOT SUPPORTED)\n");
---- canu.orig/src/overlapInCore/overlapInCorePartition.C
-+++ canu/src/overlapInCore/overlapInCorePartition.C
-@@ -355,7 +355,7 @@
- if (err) {
- fprintf(stderr, "usage: %s [opts]\n", argv[0]);
- fprintf(stderr, " Someone should write the command line help.\n");
-- fprintf(stderr, " But this is only used interally to canu, so...\n");
-+ fprintf(stderr, " But this is only used internally to canu, so...\n");
- exit(1);
- }
-
---- canu.orig/src/stores/ovStore.C
-+++ canu/src/stores/ovStore.C
-@@ -122,7 +122,7 @@
- ovlLen = loadOverlapsForRead(tid, ovl, ovlMax);
-
- if (ovlLen != nopr[tid]) {
-- fprintf(stderr, "ERRROR: Failed loading overlaps for read %u: expected %u overlaps, loaded %u.\n",
-+ fprintf(stderr, "ERROR: Failed loading overlaps for read %u: expected %u overlaps, loaded %u.\n",
- tid, nopr[tid], ovlLen);
- exit(1);
- }
---- canu.orig/src/utility/src/utility/intervalList.H
-+++ canu/src/utility/src/utility/intervalList.H
-@@ -102,12 +102,12 @@
+--- canu.orig/src/utility/src/datastructures/intervalList-v1.H
++++ canu/src/utility/src/datastructures/intervalList-v1.H
+@@ -103,12 +103,12 @@
intervalList<iNum>::add(iNum position, iNum length) {
if (length < 0) {
=====================================
debian/patches/stacktrace
=====================================
@@ -2,20 +2,9 @@ Author: Michael R. Crusoe <crusoe at debian.org>
Description: ignore broken GCC version check
Forwarded: not-needed
---- a/src/Makefile
-+++ b/src/Makefile
-@@ -229,7 +229,7 @@ ifeq (${CANU_BUILD_ENV}, ports)
- CXXFLAGS += -pthread -fopenmp -fPIC
- CFLAGS += -pthread -fopenmp -fPIC
- LDFLAGS += -pthread -fopenmp -lm
-- LDLIBS += -lsnappy
-+ LDLIBS += -lsnappy -lbacktrace
- else
- CC ?= cc
- CXX ?= c++
---- a/src/main.mk
-+++ b/src/main.mk
-@@ -170,22 +170,6 @@ SOURCES += utility/src/htslib/hts/b
+--- canu.orig/src/main.mk
++++ canu/src/main.mk
+@@ -170,22 +170,6 @@
utility/src/htslib/htscodecs/tokenise_name3.c \
utility/src/htslib/htscodecs/utils.c
@@ -38,3 +27,12 @@ Forwarded: not-needed
SRC_INCDIRS := utility/src \
stores \
stores/libsnappy \
+@@ -194,7 +178,7 @@
+
+ SYS_INCDIRS += $(shell pkg-config --cflags-only-I openssl libcurl liblzma | sed s:-I/:/:g)
+ LDFLAGS += $(shell pkg-config --libs-only-L openssl libcurl liblzma)
+-LDLIBS += $(shell pkg-config --libs-only-l openssl libcurl liblzma) -lz -lbz2 -lsnappy
++LDLIBS += $(shell pkg-config --libs-only-l openssl libcurl liblzma) -lz -lbz2 -lsnappy -lbacktrace
+
+ SUBMAKEFILES := stores/dumpBlob.mk \
+ stores/ovStoreBuild.mk \
=====================================
debian/patches/use-debian-mhap-at-runtime.patch
=====================================
@@ -2,9 +2,9 @@ Description: Use mhap jar from /usr/share/java
Author: Afif Elghraoui <afif at debian.org>
Forwarded: not-needed
Last-Update: 2016-03-20
---- a/src/pipelines/canu/OverlapMhap.pm
-+++ b/src/pipelines/canu/OverlapMhap.pm
-@@ -344,7 +344,7 @@ sub mhapConfigure ($$$) {
+--- canu.orig/src/pipelines/canu/OverlapMhap.pm
++++ canu/src/pipelines/canu/OverlapMhap.pm
+@@ -344,7 +344,7 @@
print F "cd ./blocks\n";
print F "\n";
print F "\$je $javaOpt -XX:ParallelGCThreads=", getGlobal("${tag}mhapThreads"), " -server -Xms", $javaMemory, "m -Xmx", $javaMemory, "m \\\n";
@@ -13,7 +13,7 @@ Last-Update: 2016-03-20
print F " --repeat-weight 0.9 --repeat-idf-scale 10 -k $merSize \\\n";
print F " --supress-noise 2 \\\n" if (defined(getGlobal("${tag}MhapFilterUnique")) && getGlobal("${tag}MhapFilterUnique") == 1);
print F " --no-tf \\\n" if (defined(getGlobal("${tag}MhapNoTf")) && getGlobal("${tag}MhapNoTf") == 1);
-@@ -467,7 +467,7 @@ sub mhapConfigure ($$$) {
+@@ -467,7 +467,7 @@
print F " # Start up the producer.\n";
print F " \$je $javaOpt -XX:ParallelGCThreads=", getGlobal("${tag}mhapThreads"), " -server -Xms", $javaMemory, "m -Xmx", $javaMemory, "m \\\n";
@@ -22,3 +22,33 @@ Last-Update: 2016-03-20
print F " --repeat-weight 0.9 --repeat-idf-scale 10 -k $merSize \\\n";
print F " --supress-noise 2 \\\n" if (defined(getGlobal("${tag}MhapFilterUnique")) && getGlobal("${tag}MhapFilterUnique") == 1);
print F " --no-tf \\\n" if (defined(getGlobal("${tag}MhapNoTf")) && getGlobal("${tag}MhapNoTf") == 1);
+--- canu.orig/src/main.mk
++++ canu/src/main.mk
+@@ -267,7 +267,6 @@
+ pipelines/draw-tig.pl -> bin/draw-tig
+
+ FILES += pipelines/canu.defaults -> bin/canu.defaults \
+- mhap/mhap-2.1.3.jar -> share/java/classes/mhap-2.1.3.jar \
+ pipelines/canu/Consensus.pm -> lib/perl5/site_perl/canu/Consensus.pm \
+ pipelines/canu/CorrectReads.pm -> lib/perl5/site_perl/canu/CorrectReads.pm \
+ pipelines/canu/HaplotypeReads.pm -> lib/perl5/site_perl/canu/HaplotypeReads.pm \
+--- canu.orig/src/pipelines/canu/Defaults.pm
++++ canu/src/pipelines/canu/Defaults.pm
+@@ -797,7 +797,7 @@
+ $global{"availablehosts"} = undef; # Internal list of cpus-memory-nodes describing the grid.
+
+ $global{"perl"} = $^X; # Use whatever perl interpreter is in use now for resubmission.
+- $global{"perl"} = `command -v perl` if (!defined($global{"perl"}));
++ $global{"perl"} = `which perl` if (!defined($global{"perl"}));
+
+ $global{"localmemory"} = 0; # Amount of memory on the local host, set in Grid_Local.pm
+ $global{"localthreads"} = 0;
+@@ -1075,7 +1075,7 @@
+ (getGlobal("utgOverlapper") ne "mhap"));
+
+ $java = getGlobal("java");
+- $java = `command -v $java`; # See Execution.pm getBinDirectoryShellCode()
++ $java = `which $java`; # See Execution.pm getBinDirectoryShellCode()
+ $java =~ s/^\s+//;
+ $java =~ s/\s+$//;
+
View it on GitLab: https://salsa.debian.org/med-team/canu/-/compare/5b87adb006dfd9cfb13dcd27a59b1594fad3b00a...e802089000cda1484a25bbad1b7ceb5eb05fe590
--
View it on GitLab: https://salsa.debian.org/med-team/canu/-/compare/5b87adb006dfd9cfb13dcd27a59b1594fad3b00a...e802089000cda1484a25bbad1b7ceb5eb05fe590
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