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subread: Document patches, test on RHEL, clean up
Module Name: pkgsrc-wip
Committed By: Jason W. Bacon <bacon4000%gmail.com@localhost>
Pushed By: outpaddling
Date: Mon Jan 20 10:59:16 2025 -0600
Changeset: 1d42c7402f0cd73f405a023c99cc23ed82156bce
Modified Files:
subread/DESCR
subread/Makefile
subread/distinfo
subread/patches/patch-HelperFunctions.c
subread/patches/patch-core-junction.c
subread/patches/patch-gene-algorithms.c
subread/patches/patch-input-files.c
subread/patches/patch-long-hashtable.c
subread/patches/patch-longread-one_LRMsorted-hashtable.c
subread/patches/patch-longread-one_Makefile
subread/patches/patch-longread-one_longread-mapping.c
subread/patches/patch-read-repair.c
subread/patches/patch-sorted-hashtable.c
Log Message:
subread: Document patches, test on RHEL, clean up
To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=1d42c7402f0cd73f405a023c99cc23ed82156bce
Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.
diffstat:
subread/DESCR | 34 +++++++++++++---------
subread/Makefile | 15 +++++-----
subread/distinfo | 20 ++++++-------
subread/patches/patch-HelperFunctions.c | 4 +++
subread/patches/patch-core-junction.c | 4 +++
subread/patches/patch-gene-algorithms.c | 4 +++
subread/patches/patch-input-files.c | 4 +++
subread/patches/patch-long-hashtable.c | 4 +++
.../patch-longread-one_LRMsorted-hashtable.c | 4 +++
subread/patches/patch-longread-one_Makefile | 4 +++
.../patches/patch-longread-one_longread-mapping.c | 4 +++
subread/patches/patch-read-repair.c | 4 +++
subread/patches/patch-sorted-hashtable.c | 4 +++
13 files changed, 79 insertions(+), 30 deletions(-)
diffs:
diff --git a/subread/DESCR b/subread/DESCR
index dffe014722..4b41ed5fd5 100644
--- a/subread/DESCR
+++ b/subread/DESCR
@@ -1,13 +1,21 @@
-The Subread package comprises a suite of software programs for processing
-next-gen sequencing read data including:
- Subread: a general-purpose read aligner which can align both genomic
- DNA-seq and RNA-seq reads. It can also be used to discover genomic
- mutations including short indels and structural variants.
- Subjunc: a read aligner developed for aligning RNA-seq reads and for the
- detection of exon-exon junctions. Gene fusion events can be detected as
- well.
- featureCounts: a software program developed for counting reads to genomic
- features such as genes, exons, promoters and genomic bins.
- Sublong: a long-read aligner that is designed based on seed-and-vote.
- exactSNP: a SNP caller that discovers SNPs by testing signals against local
- background noises.
+The Subread package comprises a suite of software programs for
+processing next-gen sequencing read data including:
+
+ Subread: a general-purpose read aligner which can align both
+ genomic DNA-seq and RNA-seq reads. It can also be used to
+ discover genomic mutations including short indels and structural
+ variants.
+
+ Subjunc: a read aligner developed for aligning RNA-seq reads
+ and for the detection of exon-exon junctions. Gene fusion events
+ can be detected as well.
+
+ featureCounts: a software program developed for counting
+ reads to genomic features such as genes, exons, promoters and
+ genomic bins.
+
+ Sublong: a long-read aligner that is designed based on
+ seed-and-vote.
+
+ exactSNP: a SNP caller that discovers SNPs by testing signals
+ against local background noises.
diff --git a/subread/Makefile b/subread/Makefile
index f3b088c6ad..f19fae8258 100644
--- a/subread/Makefile
+++ b/subread/Makefile
@@ -1,12 +1,5 @@
# $NetBSD$
-# Subread is designed to issue a warning if free memory is below 3 GiB.
-# It currently does not check free memory on NetBSD due to the lack of
-# libsysinfo. We could add NetBSD-specific code, but it would be a better use
-# of time to port libsysinfo to NetBSD since it's useful for other apps.
-# The libsysinfo package is only for SunOS at the time of this writing.
-# FreeBSD has a libsysinfo port that may serve as a model for NetBSD.
-
DISTNAME= subread-2.0.8-source
PKGNAME= subread-2.0.8
CATEGORIES= biology
@@ -17,6 +10,14 @@ HOMEPAGE= https://subread.sourceforge.net/
COMMENT= High-performance read alignment, quantification and mutation discovery
LICENSE= gnu-gpl-v3
+# Subread is designed to issue a warning if free memory is below 3 GiB.
+# It currently does not check free memory on NetBSD due to the lack of
+# libsysinfo. We could add NetBSD-specific code, but it would be a better use
+# of time to port libsysinfo to NetBSD since it's useful for other apps.
+# The libsysinfo package is only for SunOS at the time of this writing.
+# FreeBSD has a libsysinfo port that may serve as a model for NetBSD.
+NOT_FOR_PLATFORMS+= NetBSD-*-*
+
USE_TOOLS+= gmake
WRKSRC= ${WRKDIR}/subread-2.0.8-source/src
diff --git a/subread/distinfo b/subread/distinfo
index 90f2b4aa26..5fd8e09618 100644
--- a/subread/distinfo
+++ b/subread/distinfo
@@ -3,15 +3,15 @@ $NetBSD$
BLAKE2s (subread-2.0.8-source.tar.gz) = ddf9b8e627210aa133e019496deb90fdba8a387585ca9403fa630192f44211ee
SHA512 (subread-2.0.8-source.tar.gz) = 740c14243fbf24ccd7316966788575f8f310a442acd8bb978e330797805b9568fb719cde28afb9e747170c92835b1661c12ce045e3bf1452a71e0286d73a0ad7
Size (subread-2.0.8-source.tar.gz) = 26074498 bytes
-SHA1 (patch-HelperFunctions.c) = e3cc55a2844ad8fbc415fa6e3f112f39bd83b276
-SHA1 (patch-core-junction.c) = f05d63e7949e30b4d40160858823369be675ae59
-SHA1 (patch-gene-algorithms.c) = 37b1334ed733f7cd6e1b905f4bb065e8f003207c
-SHA1 (patch-input-files.c) = 278661cee86525d258b6a1109c82c7cc0e1990e4
-SHA1 (patch-long-hashtable.c) = 24046bcb0a2f3e1157d3922c4f50ffb4404089df
-SHA1 (patch-longread-one_LRMsorted-hashtable.c) = 434bf36fa170ed51409e51b2e037c5ec722e9305
-SHA1 (patch-longread-one_Makefile) = 0855b1a0cc81b50e0e621bd3f4c86d227f7623c0
-SHA1 (patch-longread-one_longread-mapping.c) = e2a2f3170063fc7d6e1e1af6f2f04c4c6bb601db
-SHA1 (patch-read-repair.c) = 91b67022053738e0e669f176a42dca51d7bb1bf2
+SHA1 (patch-HelperFunctions.c) = d54debdba0a3a71cced2463aeef65bfe05dc9dfe
+SHA1 (patch-core-junction.c) = 481cd069aa42d673bbc10c80bb9548547e808b0c
+SHA1 (patch-gene-algorithms.c) = 42e879e95bd22eb34973ec5f87105c18dcac82b7
+SHA1 (patch-input-files.c) = 5fbaf9c38d7fdff74b9227b79db82865c03abcd6
+SHA1 (patch-long-hashtable.c) = 3fcc2e0b7c8564b329a9d4582caaed025e7832b2
+SHA1 (patch-longread-one_LRMsorted-hashtable.c) = d46ea9b73dee4f0531a002c22099865e3cce1034
+SHA1 (patch-longread-one_Makefile) = 138e6cf370a1b566738eb98793d40a61b4837320
+SHA1 (patch-longread-one_longread-mapping.c) = de09092da544f2286f4a5fee7a70c08135e44b40
+SHA1 (patch-read-repair.c) = 4d7085ec8558647c7d92f5d0697b04b526496a75
SHA1 (patch-sambam-file.c) = 16d3bf05718db64518cfd94e6574b2c3a0794c79
-SHA1 (patch-sorted-hashtable.c) = 563f376063159387f2411286d5c4f145541148aa
+SHA1 (patch-sorted-hashtable.c) = 36d4668a3fac89b7b8fa750197962d17deaa4ed5
SHA1 (patch-subread.h) = b3d27a6f964ffece4b51ec59d5fd95fbd6ead160
diff --git a/subread/patches/patch-HelperFunctions.c b/subread/patches/patch-HelperFunctions.c
index e10e44273b..d8f0cfe584 100644
--- a/subread/patches/patch-HelperFunctions.c
+++ b/subread/patches/patch-HelperFunctions.c
@@ -1,3 +1,7 @@
+$NetBSD$
+
+# Use standard compiler macros
+
--- HelperFunctions.c.orig 2020-06-04 23:58:40 UTC
+++ HelperFunctions.c
@@ -845,7 +845,7 @@ int strcmp_number(char * s1, char * s2)
diff --git a/subread/patches/patch-core-junction.c b/subread/patches/patch-core-junction.c
index 44567984a1..408f848df7 100644
--- a/subread/patches/patch-core-junction.c
+++ b/subread/patches/patch-core-junction.c
@@ -1,3 +1,7 @@
+$NetBSD$
+
+# Portability
+
--- core-junction.c.orig 2018-11-08 15:19:02 UTC
+++ core-junction.c
@@ -22,6 +22,7 @@
diff --git a/subread/patches/patch-gene-algorithms.c b/subread/patches/patch-gene-algorithms.c
index d8bfc0d449..0d2ae0ea1f 100644
--- a/subread/patches/patch-gene-algorithms.c
+++ b/subread/patches/patch-gene-algorithms.c
@@ -1,3 +1,7 @@
+$NetBSD$
+
+# Use standard compiler macros
+
--- gene-algorithms.c.orig 2021-03-30 13:51:05 UTC
+++ gene-algorithms.c
@@ -29,7 +29,7 @@
diff --git a/subread/patches/patch-input-files.c b/subread/patches/patch-input-files.c
index 37eca1d9e7..ea69f9adef 100644
--- a/subread/patches/patch-input-files.c
+++ b/subread/patches/patch-input-files.c
@@ -1,3 +1,7 @@
+$NetBSD$
+
+# Add FreeBSD support
+
--- input-files.c.orig 2020-06-05 00:33:03 UTC
+++ input-files.c
@@ -48,7 +48,7 @@ FILE * f_subr_open(const char * fname, const char * mo
diff --git a/subread/patches/patch-long-hashtable.c b/subread/patches/patch-long-hashtable.c
index cfb9557fa6..d3ef8788a1 100644
--- a/subread/patches/patch-long-hashtable.c
+++ b/subread/patches/patch-long-hashtable.c
@@ -1,3 +1,7 @@
+$NetBSD$
+
+# Use standard compiler macros
+
--- long-hashtable.c.orig 2020-06-04 23:59:33 UTC
+++ long-hashtable.c
@@ -22,7 +22,7 @@
diff --git a/subread/patches/patch-longread-one_LRMsorted-hashtable.c b/subread/patches/patch-longread-one_LRMsorted-hashtable.c
index f5cfe3d3cb..c661697cb3 100644
--- a/subread/patches/patch-longread-one_LRMsorted-hashtable.c
+++ b/subread/patches/patch-longread-one_LRMsorted-hashtable.c
@@ -1,3 +1,7 @@
+$NetBSD$
+
+# Use standard compiler macros
+
--- longread-one/LRMsorted-hashtable.c.orig 2018-11-08 14:47:43 UTC
+++ longread-one/LRMsorted-hashtable.c
@@ -22,11 +22,9 @@
diff --git a/subread/patches/patch-longread-one_Makefile b/subread/patches/patch-longread-one_Makefile
index 41a2a468ea..dc5020ca59 100644
--- a/subread/patches/patch-longread-one_Makefile
+++ b/subread/patches/patch-longread-one_Makefile
@@ -1,3 +1,7 @@
+$NetBSD$
+
+# Respect env
+
--- longread-one/Makefile.orig 2024-07-25 00:35:55 UTC
+++ longread-one/Makefile
@@ -1,12 +1,12 @@
diff --git a/subread/patches/patch-longread-one_longread-mapping.c b/subread/patches/patch-longread-one_longread-mapping.c
index 4db4bfa499..29346060d1 100644
--- a/subread/patches/patch-longread-one_longread-mapping.c
+++ b/subread/patches/patch-longread-one_longread-mapping.c
@@ -1,3 +1,7 @@
+$NetBSD$
+
+# Add FreeBSD support
+
--- longread-one/longread-mapping.c.orig 2021-03-30 13:58:29 UTC
+++ longread-one/longread-mapping.c
@@ -30,7 +30,9 @@
diff --git a/subread/patches/patch-read-repair.c b/subread/patches/patch-read-repair.c
index aebf9c9449..df2dbf8afb 100644
--- a/subread/patches/patch-read-repair.c
+++ b/subread/patches/patch-read-repair.c
@@ -1,3 +1,7 @@
+$NetBSD$
+
+# Portability
+
--- read-repair.c.orig 2018-11-08 15:20:06 UTC
+++ read-repair.c
@@ -3,6 +3,7 @@
diff --git a/subread/patches/patch-sorted-hashtable.c b/subread/patches/patch-sorted-hashtable.c
index 9a3637e942..0c385347d5 100644
--- a/subread/patches/patch-sorted-hashtable.c
+++ b/subread/patches/patch-sorted-hashtable.c
@@ -1,3 +1,7 @@
+$NetBSD$
+
+# Use standard compiler macros
+
--- sorted-hashtable.c.orig 2018-11-08 03:33:50 UTC
+++ sorted-hashtable.c
@@ -23,11 +23,9 @@
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