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necat: import necat version 0.0.1_update20200803 as wip/necat
Module Name: pkgsrc-wip
Committed By: Brook Milligan <brook%nmsu.edu@localhost>
Pushed By: brook
Date: Fri Jun 4 10:35:04 2021 -0600
Changeset: e06f8b998bab4784193ed2e034f7dd0bdaef1126
Modified Files:
Makefile
Added Files:
necat/DESCR
necat/Makefile
necat/PLIST
necat/distinfo
necat/patches/patch-Makefile
necat/patches/patch-pipeline_main.mk
Log Message:
necat: import necat version 0.0.1_update20200803 as wip/necat
NECAT is an error correction and *de-novo* assembly tool for Nanopore
long noisy reads.
To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=e06f8b998bab4784193ed2e034f7dd0bdaef1126
Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.
diffstat:
Makefile | 1 +
necat/DESCR | 2 ++
necat/Makefile | 42 ++++++++++++++++++++++++++
necat/PLIST | 57 ++++++++++++++++++++++++++++++++++++
necat/distinfo | 8 +++++
necat/patches/patch-Makefile | 18 ++++++++++++
necat/patches/patch-pipeline_main.mk | 14 +++++++++
7 files changed, 142 insertions(+)
diffs:
diff --git a/Makefile b/Makefile
index 024429caf4..9d0d2fbabf 100644
--- a/Makefile
+++ b/Makefile
@@ -2482,6 +2482,7 @@ SUBDIR+= ncp
SUBDIR+= ncrack
SUBDIR+= neb-cd512
SUBDIR+= neb-hdtoolbox
+SUBDIR+= necat
SUBDIR+= necpp-git
SUBDIR+= nehe-opengl-tutorials
SUBDIR+= nemo
diff --git a/necat/DESCR b/necat/DESCR
new file mode 100644
index 0000000000..2fd4b81f08
--- /dev/null
+++ b/necat/DESCR
@@ -0,0 +1,2 @@
+NECAT is an error correction and *de-novo* assembly tool for Nanopore
+long noisy reads.
diff --git a/necat/Makefile b/necat/Makefile
new file mode 100644
index 0000000000..9e4afeb60b
--- /dev/null
+++ b/necat/Makefile
@@ -0,0 +1,42 @@
+# $NetBSD$
+
+GITHUB_PROJECT= NECAT
+GITHUB_TAG= refs/tags/v0.0.1_update20200803
+DISTNAME= v0.0.1_update20200803
+PKGNAME= ${GITHUB_PROJECT:tl}-${DISTNAME:S,^v,,:S,_update,.,}
+CATEGORIES= biology
+MASTER_SITES= ${MASTER_SITE_GITHUB:=xiaochuanle/}
+DIST_SUBDIR= ${GITHUB_PROJECT}
+
+MAINTAINER= pkgsrc-users%NetBSD.org@localhost
+HOMEPAGE= https://github.com/xiaochuanle/NECAT/
+COMMENT= Error correction and de-novo assembler Nanopore reads
+#LICENSE= # TODO: (see mk/license.mk)
+
+WRKSRC= ${WRKDIR}/NECAT-0.0.1_update20200803/src
+USE_LANGUAGES= c c++
+USE_TOOLS+= gmake pax perl:run
+
+REPLACE_PERL= pipeline/necat.pl
+
+REPLACE_SH+= scripts/oc2asmpm.sh
+REPLACE_SH+= scripts/oc2cmd.sh
+REPLACE_SH+= scripts/oc2cns.sh
+REPLACE_SH+= scripts/oc2cns_iter.sh
+REPLACE_SH+= scripts/oc2ctgpm.sh
+REPLACE_SH+= scripts/oc2trim.sh
+REPLACE_SH+= scripts/oc2trim_bases.sh
+REPLACE_SH+= scripts/ontsa.sh
+
+INSTALLATION_DIRS+= bin
+
+do-install:
+ cd ${WRKSRC}/../${OPSYS}-${MACHINE_ARCH}/bin && ${PAX} -rw . ${DESTDIR}${PREFIX}/bin
+ ${CHMOD} a-x ${DESTDIR}${PREFIX}/bin/refmap.sh
+ ${CHMOD} a-x ${DESTDIR}${PREFIX}/bin/run_ctgpm.sh
+ # ${RM} -r ${DESTDIR}${PREFIX}/bin/Plgd
+ ${RM} -r ${DESTDIR}${PREFIX}/bin/trim_bases_accurate
+ ${RM} -r ${DESTDIR}${PREFIX}/bin/trim_bases_accurate0
+ ${RM} ${DESTDIR}${PREFIX}/bin/test.sh
+
+.include "../../mk/bsd.pkg.mk"
diff --git a/necat/PLIST b/necat/PLIST
new file mode 100644
index 0000000000..73b7d7208c
--- /dev/null
+++ b/necat/PLIST
@@ -0,0 +1,57 @@
+@comment $NetBSD$
+bin/Necat.pm
+bin/Plgd/Grid.pm
+bin/Plgd/GridLsf.pm
+bin/Plgd/GridPbs.pm
+bin/Plgd/GridSge.pm
+bin/Plgd/GridSlurm.pm
+bin/Plgd/Project.pm
+bin/Plgd/Script.pm
+bin/Plgd/Utils.pm
+bin/ctgcns
+bin/filter_m4
+bin/fsa_assemble
+bin/fsa_ctg_bridge
+bin/fsa_ol_filter
+bin/fsa_rd_extract
+bin/fsa_rd_stat
+bin/fsa_rd_tools
+bin/libfsa.a
+bin/libontcns.a
+bin/necat.pl
+bin/necat.sh
+bin/oc2FixCanInfo
+bin/oc2ReorderCnsReads
+bin/oc2SplitCtgs
+bin/oc2asmpm
+bin/oc2asmpm.sh
+bin/oc2cmd.sh
+bin/oc2cns
+bin/oc2cns.sh
+bin/oc2cns_iter.sh
+bin/oc2ctgpm
+bin/oc2ctgpm.sh
+bin/oc2elr
+bin/oc2etr
+bin/oc2lcr
+bin/oc2mkdb
+bin/oc2orderResults
+bin/oc2pcan
+bin/oc2pm
+bin/oc2pm4
+bin/oc2pmov
+bin/oc2pprr
+bin/oc2renumberSeqs
+bin/oc2rm
+bin/oc2rm_worker
+bin/oc2slr
+bin/oc2slstats
+bin/oc2test
+bin/oc2trim.sh
+bin/oc2trimBases
+bin/oc2trim_bases.sh
+bin/ontsa.sh
+bin/pigz
+bin/pm4
+bin/refmap.sh
+bin/run_ctgpm.sh
diff --git a/necat/distinfo b/necat/distinfo
new file mode 100644
index 0000000000..5c2ac0ae5f
--- /dev/null
+++ b/necat/distinfo
@@ -0,0 +1,8 @@
+$NetBSD$
+
+SHA1 (NECAT/v0.0.1_update20200803.tar.gz) = d35904ed2ef79dbcfe0a7757825e39b6da49c114
+RMD160 (NECAT/v0.0.1_update20200803.tar.gz) = 0d52e27e37ee309ddbd1434a1d245b089dfd7d24
+SHA512 (NECAT/v0.0.1_update20200803.tar.gz) = 77b5256deb480711132adfdb8763bc1247046592e2bbecacc59934a1188f49af6d8ee678e8278606aa859417fbe5c76364c627dacbdf3e3ec0bdb8a052469690
+Size (NECAT/v0.0.1_update20200803.tar.gz) = 500777 bytes
+SHA1 (patch-Makefile) = f6c03c52eaf50ba0ab8ddea39691a64805c6bb8f
+SHA1 (patch-pipeline_main.mk) = 31568393708ea14a8346f5874ef3fdb9f2f24c93
diff --git a/necat/patches/patch-Makefile b/necat/patches/patch-Makefile
new file mode 100644
index 0000000000..2b42509862
--- /dev/null
+++ b/necat/patches/patch-Makefile
@@ -0,0 +1,18 @@
+$NetBSD$
+
+Do not change MACHINETYPE needlessly. Doing so prevents easy
+discovery of the build directory.
+
+--- Makefile.orig 2020-08-03 07:31:39.000000000 +0000
++++ Makefile
+@@ -344,10 +344,6 @@ OSTYPE := $(shell echo `uname`)
+ OSVERSION := $(shell echo `uname -r`)
+ MACHINETYPE := $(shell echo `uname -m`)
+
+-ifeq (${MACHINETYPE}, x86_64)
+- MACHINETYPE = amd64
+-endif
+-
+ ifeq (${MACHINETYPE}, Power Macintosh)
+ MACHINETYPE = ppc
+ endif
diff --git a/necat/patches/patch-pipeline_main.mk b/necat/patches/patch-pipeline_main.mk
new file mode 100644
index 0000000000..9e42ee2392
--- /dev/null
+++ b/necat/patches/patch-pipeline_main.mk
@@ -0,0 +1,14 @@
+$NetBSD$
+
+Do not set execute permissions on a non-executable file.
+
+--- pipeline/main.mk.orig 2020-08-03 07:31:39.000000000 +0000
++++ pipeline/main.mk
+@@ -23,7 +23,6 @@ ${TARGET_DIR}/Necat.pm: pipeline/Necat.p
+ ${TARGET_DIR}/necat.sh: pipeline/necat.sh
+ @if [ ! -e ${TARGET_DIR} ] ; then mkdir -p ${TARGET_DIR} ; fi
+ cp -pf pipeline/necat.sh ${TARGET_DIR}/necat.sh
+- chmod +x ${TARGET_DIR}/necat.sh
+
+ ${TARGET_DIR}/renecat.sh: pipeline/renecat.sh
+ @if [ ! -e ${TARGET_DIR} ] ; then mkdir -p ${TARGET_DIR} ; fi
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