diff options
author | V3n3RiX <venerix@redcorelinux.org> | 2017-10-09 18:53:29 +0100 |
---|---|---|
committer | V3n3RiX <venerix@redcorelinux.org> | 2017-10-09 18:53:29 +0100 |
commit | 4f2d7949f03e1c198bc888f2d05f421d35c57e21 (patch) | |
tree | ba5f07bf3f9d22d82e54a462313f5d244036c768 /sci-biology/qrna |
reinit the tree, so we can have metadata
Diffstat (limited to 'sci-biology/qrna')
-rw-r--r-- | sci-biology/qrna/Manifest | 8 | ||||
-rw-r--r-- | sci-biology/qrna/files/26qrna | 1 | ||||
-rw-r--r-- | sci-biology/qrna/files/qrna-2.0.3c-glibc-2.10.patch | 328 | ||||
-rw-r--r-- | sci-biology/qrna/files/qrna-2.0.3c-ldflags.patch | 28 | ||||
-rw-r--r-- | sci-biology/qrna/metadata.xml | 8 | ||||
-rw-r--r-- | sci-biology/qrna/qrna-2.0.3c-r2.ebuild | 58 |
6 files changed, 431 insertions, 0 deletions
diff --git a/sci-biology/qrna/Manifest b/sci-biology/qrna/Manifest new file mode 100644 index 000000000000..5b764eaffe75 --- /dev/null +++ b/sci-biology/qrna/Manifest @@ -0,0 +1,8 @@ +AUX 26qrna 30 SHA256 218d879e5ef893cba33d8be7e0a6cba3f08c0a475781bbbb4c32bde6e79a32b7 SHA512 ba47d1fe1cba68ca7dce369e814a67cca24339a1ec213d206001b4f87f8939d81c7e59bc285090e5ec2cec05693f560c9c4883cae8f67891f6053d9bc69cc46b WHIRLPOOL 2a4d368c898fec40b1a48484b82e6ea29d9e95a8c99622bb45d59bb999813461314589bfeec2fa223b178837f69c04ea99bb8433a9481e91464d1357e0f29547 +AUX qrna-2.0.3c-glibc-2.10.patch 7571 SHA256 17f34c9e3087f2c9d2decd95e07663813087843a778db45c5be793c6b51bb82c SHA512 afa8767baadf99dafbb0ce4fa8b31017f6a12e1eadbcbd41a7e04e571d3f059395356178df3ab28f8c03c10f227123361590357c6ace6256727322ade00228e6 WHIRLPOOL ff1d1a6d0d045b406e6616512f0f2d5fbb0513a1331b475e2582e9d3eb1b4fee8b0093db01e0220bcef55470b892f57823aac8664f3ad470d5a90f91775fe37f +AUX qrna-2.0.3c-ldflags.patch 1368 SHA256 ec99724754ff3f667be139832fd871bd93f7ae0cf7247fb8d15696b0315e01d6 SHA512 4b1be14c664056eebb914e8c8223686ef0f345c860bd5aca82dced67b9580a205ef9539c563c0b0c646a9781ed0c58c4cec69d71bceb2c410dc485e9b5881c54 WHIRLPOOL 538627ab602f8f92af014e38ce5764c574f2820c7ff2c25b3f999a2e658413421c886abe7451443f907f0db52d3fdb9b6f4fb4011232e66e3ac79039dddadd13 +DIST qrna-2.0.3c.tar.bz2 6423705 SHA256 fc88b58dddab26f20477a50340453e9d360ea34956ba526f7db6959283399b1c SHA512 98710bcf8993e2c09ec1eb33632a18ac993ab817dc95a865200b0868f79b95ff61f5f7d3f0c1c33de6d26f674025ea11a8c7d8175b96071e4594daa252fa52b5 WHIRLPOOL f7c788629f6580e3f1c2ccaa5109ba13d8f103abfd3a88f3ef127577fc825fdc7deef102325ab2645a24ba1215d59b21e2c77448631c90d6eae47aa95a9463e5 +EBUILD qrna-2.0.3c-r2.ebuild 1112 SHA256 f9ca425a3e49c612341c97eec9f52c95bf295daf367acff044cc7eb95aeeadc5 SHA512 70e7e97f322970434fc5ee5abd8b75ae085fb588ea467673e01ede4b4778e819e41df83f9df1fc1d10e6ede9b52d5356519f8c4987d654f4038fbd7c5c90e853 WHIRLPOOL 0755270accc5c54d4d8a43f0f0e785c55853389fd6925ac3a7f9e7e78d05abadf88fe004aedf2b1e87c728cba96a03a9be1b9627293f47242c15ee929978860d +MISC ChangeLog 2517 SHA256 eb8cc8275ae8009fe4737eaf621bd949db65ea55ff17a5aca3798e5b57a946a8 SHA512 2f0ca6918c46768471a7aa29e5c6355a2a9704f3c21e693db9c10f9305a93bd84e5988cd8696fc7f8dba9d11b2a8b6ea32ac7816f59cc57bd930e24250cd012e WHIRLPOOL aad33d26f7cd4757b2b35a30ee87654f0f0288703069da244cd0f553ce5c9339f1072087fb4dbb27469a47055369a3e27cac72b73585dcb55c48e178ccfdf280 +MISC ChangeLog-2015 3617 SHA256 4906aebc632437f3496134b71394c1a105671779473f8d7d47be4992fcf6ae2f SHA512 e0ce33a4a9d7da21c498efb543aca316aaa9905e5b7cfc77a11cee41ee9875a102e51acb0f6d2024beee30e24a7a52acb53c61c21ec5f801142a9404ec20bff2 WHIRLPOOL a09962f8af5e6902b54ea42e76ba79faf21b6bd97ebf6dd380732bf7723531144a27077bcf1887b659e9248bd78d761cc96010f7773e2a62ab02ad67e563e54c +MISC metadata.xml 261 SHA256 15c95fe0beb2b86b616b7ac1be6f1118bd598d907b441a94d87721c0d6f36855 SHA512 537da0d3aa2741ebe4442d5dd9b53409decfc9d12ca8e5af8e737c4deb2910c884207e2d441025d19469816100889f04c11038bdffd6a1a15c6217495445090a WHIRLPOOL c00a986f98ceb4fa20ffdb0c411de9841218f8af6f7499a20a34258db4cd74cead97ef2ee18ac8cac7eae7db3c95084cbf8aa3a36f95a1ed7efbb0e088eb50c8 diff --git a/sci-biology/qrna/files/26qrna b/sci-biology/qrna/files/26qrna new file mode 100644 index 000000000000..53a90b90ed78 --- /dev/null +++ b/sci-biology/qrna/files/26qrna @@ -0,0 +1 @@ +QRNADB="/usr/share/qrna/data" diff --git a/sci-biology/qrna/files/qrna-2.0.3c-glibc-2.10.patch b/sci-biology/qrna/files/qrna-2.0.3c-glibc-2.10.patch new file mode 100644 index 000000000000..dfa1b2a29e94 --- /dev/null +++ b/sci-biology/qrna/files/qrna-2.0.3c-glibc-2.10.patch @@ -0,0 +1,328 @@ +diff -ur qrna-2.0.3c.orig/squid/sqio.c qrna-2.0.3c/squid/sqio.c +--- qrna-2.0.3c.orig/squid/sqio.c 2005-05-11 19:30:51.000000000 +0300 ++++ qrna-2.0.3c/squid/sqio.c 2009-08-05 22:27:20.000000000 +0300 +@@ -215,7 +215,7 @@ + } + + static void +-getline(struct ReadSeqVars *V) ++get_line(struct ReadSeqVars *V) + { + readline(V->f, V->sbuffer); + } +@@ -277,7 +277,7 @@ + V->seqlen = 0; + if (addfirst) addseq(V->sbuffer, V); + do { +- getline(V); ++ get_line(V); + /* feof() alone is a bug; files not necessarily \n terminated */ + if (*(V->sbuffer) == '\0' && feof(V->f)) + done = TRUE; +@@ -305,7 +305,7 @@ + char *sptr; + /* load first line of entry */ + while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0) +- getline(V); ++ get_line(V); + if (feof(V->f)) return; + + if ((sptr = strtok(V->sbuffer + 15, "\n\t ")) != NULL) +@@ -314,7 +314,7 @@ + SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID); + } + do { +- getline(V); ++ get_line(V); + if (!feof(V->f) && strncmp(V->sbuffer, "TITLE", 5) == 0) + SetSeqinfoString(V->sqinfo, V->sbuffer+15, SQINFO_DESC); + else if (!feof(V->f) && strncmp(V->sbuffer, "ACCESSION", 9) == 0) +@@ -323,7 +323,7 @@ + SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC); + } + } while (! feof(V->f) && (strncmp(V->sbuffer,"SEQUENCE", 8) != 0)); +- getline(V); /* skip next line, coords */ ++ get_line(V); /* skip next line, coords */ + + readLoop(0, endPIR, V); + +@@ -337,7 +337,7 @@ + /* get next line + */ + while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0) +- getline(V); ++ get_line(V); + } + + +@@ -355,7 +355,7 @@ + char *nm; + /* position past ';' comments */ + do { +- getline(V); ++ get_line(V); + } while (! (feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer != ';')) )); + + if (!feof(V->f)) +@@ -367,7 +367,7 @@ + } + + while (!(feof(V->f) || ((*V->sbuffer != '\0') && (*V->sbuffer == ';')))) +- getline(V); ++ get_line(V); + } + + static int +@@ -389,7 +389,7 @@ + if ((nm = strtok(V->sbuffer+16, ",\n\t ")) != NULL) + SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME); + } +- getline(V); ++ get_line(V); + } + + if (! feof(V->f)) +@@ -398,7 +398,7 @@ + /* load next line + */ + while ((!feof(V->f)) && (*V->sbuffer != ';')) +- getline(V); ++ get_line(V); + } + + +@@ -416,7 +416,7 @@ + int in_definition; + + while (strncmp(V->sbuffer, "LOCUS", 5) != 0) +- getline(V); ++ get_line(V); + + if ((sptr = strtok(V->sbuffer+12, "\n\t ")) != NULL) + { +@@ -427,7 +427,7 @@ + in_definition = FALSE; + while (! feof(V->f)) + { +- getline(V); ++ get_line(V); + if (! feof(V->f) && strstr(V->sbuffer, "DEFINITION") == V->sbuffer) + { + if ((sptr = strtok(V->sbuffer+12, "\n")) != NULL) +@@ -460,11 +460,11 @@ + + + while (!(feof(V->f) || ((*V->sbuffer!=0) && (strstr(V->sbuffer,"LOCUS") == V->sbuffer)))) +- getline(V); ++ get_line(V); + /* SRE: V->s now holds "//", so sequential + reads are wedged: fixed Tue Jul 13 1993 */ + while (!feof(V->f) && strstr(V->sbuffer, "LOCUS ") != V->sbuffer) +- getline(V); ++ get_line(V); + } + + static int +@@ -494,12 +494,12 @@ + if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL) + SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME); + +- getline(V); /*skip title-junk line*/ ++ get_line(V); /*skip title-junk line*/ + + readLoop(0, endNBRF, V); + + while (!(feof(V->f) || (*V->sbuffer != 0 && *V->sbuffer == '>'))) +- getline(V); ++ get_line(V); + } + + +@@ -529,7 +529,7 @@ + Die("bogus GCGdata format? %s", V->sbuffer); + + /* second line contains free text description */ +- getline(V); ++ get_line(V); + SetSeqinfoString(V->sqinfo, V->sbuffer, SQINFO_DESC); + + if (binary) { +@@ -549,7 +549,7 @@ + else readLoop(0, endGCGdata, V); + + while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>')))) +- getline(V); ++ get_line(V); + } + + static int +@@ -571,7 +571,7 @@ + readLoop(0, endPearson, V); + + while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>')))) +- getline(V); ++ get_line(V); + } + + +@@ -598,7 +598,7 @@ + + /* make sure we have first line */ + while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0) +- getline(V); ++ get_line(V); + + if ((sptr = strtok(V->sbuffer+5, "\n\t ")) != NULL) + { +@@ -607,7 +607,7 @@ + } + + do { +- getline(V); ++ get_line(V); + if (!feof(V->f) && strstr(V->sbuffer, "AC ") == V->sbuffer) + { + if ((sptr = strtok(V->sbuffer+5, "; \t\n")) != NULL) +@@ -631,7 +631,7 @@ + + /* load next record's ID line */ + while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0) +- getline(V); ++ get_line(V); + } + + +@@ -647,7 +647,7 @@ + { + char *sptr; + +- getline(V); /*s == "seqLen seqid string..."*/ ++ get_line(V); /*s == "seqLen seqid string..."*/ + + if ((sptr = strtok(V->sbuffer+6, " \t\n")) != NULL) + SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME); +@@ -658,7 +658,7 @@ + readLoop(0, endZuker, V); + + while (!(feof(V->f) | ((*V->sbuffer != '\0') & (*V->sbuffer == '(')))) +- getline(V); ++ get_line(V); + } + + static void +@@ -680,7 +680,7 @@ + + do { + done = feof(V->f); +- getline(V); ++ get_line(V); + if (! done) addseq(V->sbuffer, V); + } while (!done); + } +@@ -692,7 +692,7 @@ + char *sptr; + int dostruc = FALSE; + +- while (strncmp(V->sbuffer, "NAM ", 4) != 0) getline(V); ++ while (strncmp(V->sbuffer, "NAM ", 4) != 0) get_line(V); + + if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL) + SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME); +@@ -700,7 +700,7 @@ + /*CONSTCOND*/ + while (1) + { +- getline(V); ++ get_line(V); + if (feof(V->f)) {squid_errno = SQERR_FORMAT; return; } + + if (strncmp(V->sbuffer, "SRC ", 4) == 0) +@@ -732,14 +732,14 @@ + while (1) + { + /* sequence line */ +- getline(V); ++ get_line(V); + if (feof(V->f) || strncmp(V->sbuffer, "++", 2) == 0) + break; + addseq(V->sbuffer, V); + /* structure line */ + if (dostruc) + { +- getline(V); ++ get_line(V); + if (feof(V->f)) { squid_errno = SQERR_FORMAT; return; } + addstruc(V->sbuffer, V); + } +@@ -747,7 +747,7 @@ + + + while (!feof(V->f) && strncmp(V->sbuffer, "NAM ", 4) != 0) +- getline(V); ++ get_line(V); + } + + +@@ -786,7 +786,7 @@ + + /* Load the first line. + */ +- getline(dbfp); ++ get_line(dbfp); + + return dbfp; + } +@@ -800,7 +800,7 @@ + SeqfilePosition(SQFILE *sqfp, long offset) + { + fseek(sqfp->f, offset, SEEK_SET); +- getline(sqfp); ++ get_line(sqfp); + } + + +@@ -817,7 +817,7 @@ + if (sqfp->ali_aseqs != NULL) sqfp->ali_curridx = 0; + else { + rewind(sqfp->f); +- getline(sqfp); ++ get_line(sqfp); + } + } + +@@ -912,7 +912,7 @@ + do { /* skip leading comments on GCG file */ + gotuw = (strstr(V->sbuffer,"..") != NULL); + if (gotuw) readUWGCG(V); +- getline(V); ++ get_line(V); + } while (! feof(V->f)); + break; + +@@ -991,7 +991,7 @@ + do { /* skip leading comments on GCG file */ + gotuw = (strstr(V->sbuffer,"..") != NULL); + if (gotuw) readUWGCG(V); +- getline(V); ++ get_line(V); + } while (! feof(V->f)); + break; + +@@ -1098,7 +1098,7 @@ + do { /* skip leading comments on GCG file */ + gotuw = (strstr(V->sbuffer,"..") != NULL); + if (gotuw) readUWGCG(V); +- getline(V); ++ get_line(V); + } while (! feof(V->f)); + break; + +@@ -1204,7 +1204,7 @@ + do { /* skip leading comments on GCG file */ + gotuw = (strstr(V->sbuffer,"..") != NULL); + if (gotuw) readUWGCG(V); +- getline(V); ++ get_line(V); + } while (! feof(V->f)); + break; + diff --git a/sci-biology/qrna/files/qrna-2.0.3c-ldflags.patch b/sci-biology/qrna/files/qrna-2.0.3c-ldflags.patch new file mode 100644 index 000000000000..d03f650dd39e --- /dev/null +++ b/sci-biology/qrna/files/qrna-2.0.3c-ldflags.patch @@ -0,0 +1,28 @@ +diff --git a/src/Makefile b/src/Makefile +index 1d1631b..4fa3af9 100644 +--- a/src/Makefile ++++ b/src/Makefile +@@ -131,17 +131,17 @@ DEMOS = + all: $(PROGS) + + main: $(OBJ) main.o +- $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(LIBS) + cfgbuild: $(OBJ) cfgbuild.o +- $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) + eqrna: $(OBJ) eqrna.o +- $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) + eqrna_sample: $(OBJ) eqrna_sample.o +- $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) + shuffle: $(OBJ) shuffle.o +- $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) + rnamat_main: $(OBJ2) rnamat_main.o +- $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR02) $@.o $(OBJ2) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR02) $@.o $(OBJ2) $(LIBS) + + main.o: ../src/main.c + $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? diff --git a/sci-biology/qrna/metadata.xml b/sci-biology/qrna/metadata.xml new file mode 100644 index 000000000000..8417d1580d40 --- /dev/null +++ b/sci-biology/qrna/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/qrna/qrna-2.0.3c-r2.ebuild b/sci-biology/qrna/qrna-2.0.3c-r2.ebuild new file mode 100644 index 000000000000..ea79f2d548f6 --- /dev/null +++ b/sci-biology/qrna/qrna-2.0.3c-r2.ebuild @@ -0,0 +1,58 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit toolchain-funcs + +DESCRIPTION="Prototype ncRNA genefinder" +HOMEPAGE="http://selab.janelia.org/software.html" +SRC_URI="mirror://gentoo/${P}.tar.bz2" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +RDEPEND=" + dev-lang/perl + sci-biology/hmmer" +DEPEND="${RDEPEND}" + +PATCHES=( + "${FILESDIR}"/${P}-glibc-2.10.patch + "${FILESDIR}"/${P}-ldflags.patch +) + +src_prepare() { + default + sed \ + -e "s:^CC.*:CC = $(tc-getCC):" \ + -e "/^AR/s:ar:$(tc-getAR):g" \ + -e "/^RANLIB/s:ranlib:$(tc-getRANLIB):g" \ + -e "/CFLAGS/s:=.*$:= ${CFLAGS}:" \ + -i {src,squid,squid02}/Makefile || die + rm -v squid*/*.a || die +} + +src_compile() { + local d + for d in squid squid02 src; do + emake -C ${d} + done +} + +src_install() { + dobin src/{cfgbuild,eqrna,eqrna_sample,rnamat_main} scripts/* + + newdoc 00README README + dodoc -r documentation/. + + insinto /usr/share/${PN}/data + doins -r lib/. + insinto /usr/share/${PN}/demos + doins -r Demos/. + + # Sets the path to the QRNA data files + doenvd "${FILESDIR}"/26qrna +} |