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readseq: Update to latest and unbreak
Module Name: pkgsrc-wip
Committed By: Jason W. Bacon <bacon%NetBSD.org@localhost>
Pushed By: outpaddling
Date: Fri Feb 16 08:35:26 2024 -0600
Changeset: 102d893ada821806a50b31523a7bdaa29195cf60
Modified Files:
readseq/DESCR
readseq/Makefile
readseq/PLIST
readseq/distinfo
Added Files:
readseq/files/readseq.in
Removed Files:
readseq/patches/patch-aa
readseq/patches/patch-readseq.c
readseq/patches/patch-ureadseq.c
Log Message:
readseq: Update to latest and unbreak
Previous version was unfetchable
App has been reimplemented in JAVA since then
Contacted previous maintainer to see if [s]he is still interested
To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=102d893ada821806a50b31523a7bdaa29195cf60
Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.
diffstat:
readseq/DESCR | 9 +-
readseq/Makefile | 47 +++++---
readseq/PLIST | 6 +-
readseq/distinfo | 11 +-
readseq/files/readseq.in | 3 +
readseq/patches/patch-aa | 13 --
readseq/patches/patch-readseq.c | 14 ---
readseq/patches/patch-ureadseq.c | 253 ---------------------------------------
8 files changed, 43 insertions(+), 313 deletions(-)
diffs:
diff --git a/readseq/DESCR b/readseq/DESCR
index 5bbf139769..845ea2c7bc 100644
--- a/readseq/DESCR
+++ b/readseq/DESCR
@@ -1,6 +1,3 @@
-readseq is a widely used tool to convert various sequence
-data formats written by D.G. Gilbert at Indiana University,
-Bloomington. Besides the interconversion to make the
-sequences palatable for a specific application, readseq
-can be used to extract the raw sequence from any supported
-database format.
+Sequence reading library developed by the Ribosomal Database Project.
+It can handle genbank, embl, fasta, fastq, sff and sto files, can
+read from files or streams, and can handle indexing files.
diff --git a/readseq/Makefile b/readseq/Makefile
index cdf8124352..4d7e9ccfbb 100644
--- a/readseq/Makefile
+++ b/readseq/Makefile
@@ -1,25 +1,40 @@
-# $NetBSD: Makefile,v 1.5 2012/10/14 18:13:15 asau Exp $
+# $NetBSD$
#
+###########################################################
+# Generated by fbsd2pkg #
+# Fri Feb 16 07:56:47 CST 2024 #
+###########################################################
-DISTNAME= readseq
-PKGNAME= ${DISTNAME}-20031211
-CATEGORIES= local
-MASTER_SITES= ftp://ftp.ebi.ac.uk/pub/software/unix/
-EXTRACT_SUFX= .tar.Z
+DISTNAME= readseq
+PKGNAME= ${DISTNAME}-2.1.19
+CATEGORIES= biology java
+MASTER_SITES= https://downloads.sourceforge.net/project/readseq/readseq/2.1.19/
+DIST_SUBDIR= ${PKGNAME_NOREV}
+EXTRACT_SUFX= .jar
-MAINTAINER= dprice%cs.nmsu.edu@localhost
-HOMEPAGE= ftp://ftp.ebi.ac.uk/pub/software/unix/
-COMMENT= Widely Used Tool to Convert Various Sequence Formats
+OWNER= bacon%NetBSD.org@localhost
+HOMEPAGE= https://sourceforge.net/projects/readseq
+COMMENT= Read and reformat biosequences, Java command-line version
+LICENSE= public-domain
-TEST_TARGET= test
+USE_JAVA= run
+NO_BUILD= yes
+WRKSRC= ${WRKDIR}
-INSTALLATION_DIRS= bin
+SUBST_CLASSES+= java
+SUBST_STAGE.java= pre-configure
+SUBST_SED.java= -e 's|%%JAVAJARDIR%%|${JAVAJARDIR}|g'
+SUBST_SED.java+= -e 's|%%PREFIX%%|${PREFIX}|g'
+SUBST_FILES.java= ${WRKDIR}/readseq
+
+JAVAJARDIR= ${PREFIX}/share/java/classes
+INSTALLATION_DIRS= bin ${JAVAJARDIR}/readseq
+
+pre-patch:
+ ${CP} ${FILESDIR}/readseq.in ${WRKDIR}/readseq
do-install:
- ${INSTALL_PROGRAM} ${WRKSRC}/readseq ${DESTDIR}${PREFIX}/bin
- ${INSTALL_DATA_DIR} ${DESTDIR}${PREFIX}/share/doc/${DISTNAME}
- ${INSTALL_DATA} ${WRKSRC}/Formats ${DESTDIR}${PREFIX}/share/doc/${DISTNAME}
- ${INSTALL_DATA} ${WRKSRC}/Readme ${DESTDIR}${PREFIX}/share/doc/${DISTNAME}
- ${INSTALL_DATA} ${WRKSRC}/Readseq.help ${DESTDIR}${PREFIX}/share/doc/${DISTNAME}
+ ${INSTALL_DATA} ${WRKSRC}/readseq.jar ${DESTDIR}${JAVAJARDIR}/readseq
+ ${INSTALL_SCRIPT} ${WRKDIR}/readseq ${DESTDIR}${PREFIX}/bin
.include "../../mk/bsd.pkg.mk"
diff --git a/readseq/PLIST b/readseq/PLIST
index b0527fb48a..57c8fb40bd 100644
--- a/readseq/PLIST
+++ b/readseq/PLIST
@@ -1,5 +1,3 @@
-@comment $NetBSD: PLIST,v 1.2 2012/10/14 18:13:59 asau Exp $
+@comment $NetBSD$
bin/readseq
-share/doc/readseq/Formats
-share/doc/readseq/Readme
-share/doc/readseq/Readseq.help
+share/java/classes/readseq/readseq.jar
diff --git a/readseq/distinfo b/readseq/distinfo
index 87bee83730..f7da50b690 100644
--- a/readseq/distinfo
+++ b/readseq/distinfo
@@ -1,8 +1,5 @@
-$NetBSD: distinfo,v 1.3 2012/10/14 18:12:12 asau Exp $
+$NetBSD$
-RMD160 (readseq.tar.Z) = b66795ca91b942096a0af8724e16a1d79a75c9ce
-SHA512 (readseq.tar.Z) = 28ccb6ad719246dd4a4911dcb75408dccfb885ecbb931daa10fcfc1cd64bff4f64d3630607f9440da11503767886ab894dbf5478f80922f47b2c161068fc0e6a
-Size (readseq.tar.Z) = 75281 bytes
-SHA1 (patch-aa) = 16af1514f15dc612886dac68262e09d6031083fb
-SHA1 (patch-readseq.c) = d41772f54da20e08638b0e4cdf2b6c841f4a8fe1
-SHA1 (patch-ureadseq.c) = eabaf4e1f1d6a923b8d102fdc64bcee45c127c28
+BLAKE2s (readseq-2.1.19/readseq.jar) = cf04d9ae46fd396ac9e50479210049d9bb08de23ab906c7e5fc4d765a6f1fef1
+SHA512 (readseq-2.1.19/readseq.jar) = e22281882183249e6742a578e137347af9d937787e91e9db788fa6dbc9c47426b164853fe709cb7245e94940bc5c6f73b27153eda0d627cb15d4e1e56136a4d0
+Size (readseq-2.1.19/readseq.jar) = 767702 bytes
diff --git a/readseq/files/readseq.in b/readseq/files/readseq.in
new file mode 100755
index 0000000000..41d8d2466c
--- /dev/null
+++ b/readseq/files/readseq.in
@@ -0,0 +1,3 @@
+#!/bin/sh -e
+
+java -jar %%JAVAJARDIR%%/readseq.jar "$@"
diff --git a/readseq/patches/patch-aa b/readseq/patches/patch-aa
deleted file mode 100644
index d06817eb74..0000000000
--- a/readseq/patches/patch-aa
+++ /dev/null
@@ -1,13 +0,0 @@
-$NetBSD: patch-aa,v 1.1.1.1 2004/11/29 18:03:02 daprice Exp $
-
---- Makefile.orig Thu Dec 11 16:42:48 2003
-+++ Makefile
-@@ -36,7 +36,7 @@ NLDFLAGS=-I$(INCPATH) -L$(LIBPATH)
- NLIBS=$(LIB1) $(LIB2) $(OTHERLIBS)
-
-
--all: build test
-+all: build
-
- build: $(SOURCES)
- @echo "Compiling readseq..."
diff --git a/readseq/patches/patch-readseq.c b/readseq/patches/patch-readseq.c
deleted file mode 100644
index b66df7749e..0000000000
--- a/readseq/patches/patch-readseq.c
+++ /dev/null
@@ -1,14 +0,0 @@
-$NetBSD: patch-readseq.c,v 1.1 2012/10/14 18:12:13 asau Exp $
-
-Pull stdlib.h for malloc.
-
---- readseq.c.orig 1993-01-12 12:43:06.000000000 +0000
-+++ readseq.c
-@@ -161,6 +161,7 @@ link -w -o readseq -t MPST -c 'MPS ' �
-
-
-
-+#include <stdlib.h>
- #include <stdio.h>
- #include <string.h>
- #include <ctype.h>
diff --git a/readseq/patches/patch-ureadseq.c b/readseq/patches/patch-ureadseq.c
deleted file mode 100644
index 7eedc657d6..0000000000
--- a/readseq/patches/patch-ureadseq.c
+++ /dev/null
@@ -1,253 +0,0 @@
-$NetBSD: patch-ureadseq.c,v 1.1 2012/10/14 18:12:13 asau Exp $
-
-Rename "getline" to "get_line" to avoid clash with new POSIX.
-
---- ureadseq.c.orig 1993-01-12 12:43:10.000000000 +0000
-+++ ureadseq.c
-@@ -136,7 +136,7 @@ Local void readline(FILE *f, char *s, lo
- }
- }
-
--Local void getline(struct ReadSeqVars *V)
-+Local void get_line(struct ReadSeqVars *V)
- {
- readline(V->f, V->s, &V->linestart);
- }
-@@ -215,7 +215,7 @@ Local void readLoop(short margin, boolea
-
- if (addfirst) addseq(V->s, V);
- do {
-- getline(V);
-+ get_line(V);
- V->done = feof(V->f);
- V->done |= (*endTest)( &addend, &ungetend, V);
- if (V->addit && (addend || !V->done) && (strlen(V->s) > margin)) {
-@@ -246,7 +246,7 @@ Local void readIG(struct ReadSeqVars *V)
-
- while (!V->allDone) {
- do {
-- getline(V);
-+ get_line(V);
- for (si= V->s; *si != 0 && *si < ' '; si++) *si= ' '; /* drop controls */
- if (*si == 0) *V->s= 0; /* chop line to empty */
- } while (! (feof(V->f) || ((*V->s != 0) && (*V->s != ';') ) ));
-@@ -272,13 +272,13 @@ Local void readStrider(struct ReadSeqVar
- { /* ? only 1 seq/file ? */
-
- while (!V->allDone) {
-- getline(V);
-+ get_line(V);
- if (strstr(V->s,"; DNA sequence ") == V->s)
- strcpy(V->seqid, (V->s)+16);
- else
- strcpy(V->seqid, (V->s)+1);
- while ((!feof(V->f)) && (*V->s == ';')) {
-- getline(V);
-+ get_line(V);
- }
- if (feof(V->f)) V->allDone = true;
- else readLoop(0, true, endStrider, V);
-@@ -298,16 +298,16 @@ Local void readPIR(struct ReadSeqVars *V
-
- while (!V->allDone) {
- while (! (feof(V->f) || strstr(V->s,"ENTRY") || strstr(V->s,"SEQUENCE")) )
-- getline(V);
-+ get_line(V);
- strcpy(V->seqid, (V->s)+16);
- while (! (feof(V->f) || strstr(V->s,"SEQUENCE") == V->s))
-- getline(V);
-+ get_line(V);
- readLoop(0, false, endPIR, V);
-
- if (!V->allDone) {
- while (! (feof(V->f) || ((*V->s != 0)
- && (strstr( V->s,"ENTRY") == V->s))))
-- getline(V);
-+ get_line(V);
- }
- if (feof(V->f)) V->allDone = true;
- }
-@@ -327,13 +327,13 @@ Local void readGenBank(struct ReadSeqVar
- while (!V->allDone) {
- strcpy(V->seqid, (V->s)+12);
- while (! (feof(V->f) || strstr(V->s,"ORIGIN") == V->s))
-- getline(V);
-+ get_line(V);
- readLoop(0, false, endGB, V);
-
- if (!V->allDone) {
- while (! (feof(V->f) || ((*V->s != 0)
- && (strstr( V->s,"LOCUS") == V->s))))
-- getline(V);
-+ get_line(V);
- }
- if (feof(V->f)) V->allDone = true;
- }
-@@ -364,11 +364,11 @@ Local void readNBRF(struct ReadSeqVars *
- {
- while (!V->allDone) {
- strcpy(V->seqid, (V->s)+4);
-- getline(V); /*skip title-junk line*/
-+ get_line(V); /*skip title-junk line*/
- readLoop(0, false, endNBRF, V);
- if (!V->allDone) {
- while (!(feof(V->f) || (*V->s != 0 && *V->s == '>')))
-- getline(V);
-+ get_line(V);
- }
- if (feof(V->f)) V->allDone = true;
- }
-@@ -390,7 +390,7 @@ Local void readPearson(struct ReadSeqVar
- readLoop(0, false, endPearson, V);
- if (!V->allDone) {
- while (!(feof(V->f) || ((*V->s != 0) && (*V->s == '>'))))
-- getline(V);
-+ get_line(V);
- }
- if (feof(V->f)) V->allDone = true;
- }
-@@ -410,14 +410,14 @@ Local void readEMBL(struct ReadSeqVars *
- while (!V->allDone) {
- strcpy(V->seqid, (V->s)+5);
- do {
-- getline(V);
-+ get_line(V);
- } while (!(feof(V->f) | (strstr(V->s,"SQ ") == V->s)));
-
- readLoop(0, false, endEMBL, V);
- if (!V->allDone) {
- while (!(feof(V->f) |
- ((*V->s != '\0') & (strstr(V->s,"ID ") == V->s))))
-- getline(V);
-+ get_line(V);
- }
- if (feof(V->f)) V->allDone = true;
- }
-@@ -437,13 +437,13 @@ Local void readZuker(struct ReadSeqVars
- /*! 1st string is Zuker's Fortran format */
-
- while (!V->allDone) {
-- getline(V); /*s == "seqLen seqid string..."*/
-+ get_line(V); /*s == "seqLen seqid string..."*/
- strcpy(V->seqid, (V->s)+6);
- readLoop(0, false, endZuker, V);
- if (!V->allDone) {
- while (!(feof(V->f) |
- ((*V->s != '\0') & (*V->s == '('))))
-- getline(V);
-+ get_line(V);
- }
- if (feof(V->f)) V->allDone = true;
- }
-@@ -486,7 +486,7 @@ Local void readPlain(struct ReadSeqVars
- do {
- addseq(V->s, V);
- V->done = feof(V->f);
-- getline(V);
-+ get_line(V);
- } while (!V->done);
- if (V->choice == kListSequences) addinfo(V->seqid, V);
- V->allDone = true;
-@@ -512,7 +512,7 @@ Local void readUWGCG(struct ReadSeqVars
- else if (si = strstr(V->seqid,"..")) *si = 0;
- do {
- V->done = feof(V->f);
-- getline(V);
-+ get_line(V);
- if (!V->done) addseq((V->s), V);
- } while (!V->done);
- if (V->choice == kListSequences) addinfo(V->seqid, V);
-@@ -531,7 +531,7 @@ Local void readOlsen(struct ReadSeqVars
- if (V->addit) V->seqlen = 0;
- rewind(V->f); V->nseq= 0;
- do {
-- getline(V);
-+ get_line(V);
- V->done = feof(V->f);
-
- if (V->done && !(*V->s)) break;
-@@ -614,7 +614,7 @@ Local void readMSF(struct ReadSeqVars *V
- if (V->addit) V->seqlen = 0;
- rewind(V->f); V->nseq= 0;
- do {
-- getline(V);
-+ get_line(V);
- V->done = feof(V->f);
-
- if (V->done && !(*V->s)) break;
-@@ -683,7 +683,7 @@ Local void readPAUPinterleaved(struct Re
- domatch= (V->matchchar > 0);
-
- do {
-- getline(V);
-+ get_line(V);
- V->done = feof(V->f);
-
- if (V->done && !(*V->s)) break;
-@@ -764,7 +764,7 @@ Local void readPAUPsequential(struct Rea
- /* rewind(V->f); V->nseq= 0; << do in caller !*/
- indata= true; /* call here after we find "matrix" */
- do {
-- getline(V);
-+ get_line(V);
- V->done = feof(V->f);
-
- if (V->done && !(*V->s)) break;
-@@ -849,7 +849,7 @@ Local void readPhylipInterleaved(struct
- /* fprintf(stderr,"Phylip-ileaf: topnseq=%d topseqlen=%d\n",V->topnseq, V->topseqlen); */
-
- do {
-- getline(V);
-+ get_line(V);
- V->done = feof(V->f);
-
- if (V->done && !(*V->s)) break;
-@@ -902,7 +902,7 @@ Local void readPhylipSequential(struct R
- while (isdigit(*si)) si++;
- skipwhitespace(si);
- V->topseqlen= atol(si);
-- getline(V);
-+ get_line(V);
- while (!V->allDone) {
- V->seqlencount= 0;
- strncpy(V->seqid, (V->s), 10);
-@@ -933,10 +933,10 @@ Local void readSeqMain(
- V->err = eFileNotFound;
- else {
-
-- for (l = skiplines_; l > 0; l--) getline( V);
-+ for (l = skiplines_; l > 0; l--) get_line( V);
-
- do {
-- getline( V);
-+ get_line( V);
- for (l= strlen(V->s); (l > 0) && (V->s[l] == ' '); l--) ;
- } while ((l == 0) && !feof(V->f));
-
-@@ -961,7 +961,7 @@ Local void readSeqMain(
- char *cp;
- /* rewind(V->f); V->nseq= 0; ?? assume it is at top ?? skiplines ... */
- while (!done) {
-- getline( V);
-+ get_line( V);
- tolowerstr( V->s);
- if (strstr( V->s, "matrix")) done= true;
- if (strstr( V->s, "interleav")) interleaved= true;
-@@ -993,7 +993,7 @@ Local void readSeqMain(
- break;
-
- case kFitch :
-- strcpy(V->seqid, V->s); getline(V);
-+ strcpy(V->seqid, V->s); get_line(V);
- readFitch(V);
- break;
-
-@@ -1001,7 +1001,7 @@ Local void readSeqMain(
- do {
- gotuw = (strstr(V->s,"..") != NULL);
- if (gotuw) readUWGCG(V);
-- getline(V);
-+ get_line(V);
- } while (!(feof(V->f) || V->allDone));
- break;
- }
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