diff options
| -rw-r--r-- | biology/embassy/Makefile | 18 | ||||
| -rw-r--r-- | biology/embassy/distinfo | 32 | ||||
| -rw-r--r-- | biology/embassy/files/domainatrix-patch-Makefile.in | 11 | ||||
| -rw-r--r-- | biology/embassy/files/emnu-patch-Makefile.in | 11 | ||||
| -rw-r--r-- | biology/embassy/pkg-plist | 48 |
5 files changed, 78 insertions, 42 deletions
diff --git a/biology/embassy/Makefile b/biology/embassy/Makefile index 34fa252f4426..4f0187c96867 100644 --- a/biology/embassy/Makefile +++ b/biology/embassy/Makefile @@ -1,3 +1,4 @@ +# ex:ts=8 # New ports collection makefile for: embassy # Date created: 1.November.2004 # Whom: Fernan Aguero <fernan@iib.unsamn.edu.ar> @@ -6,7 +7,7 @@ # PORTNAME= embassy -PORTVERSION= 2.9.0 +PORTVERSION= 2.10.0 CATEGORIES= biology MASTER_SITES= ftp://ftp.uk.embnet.org/pub/EMBOSS/ \ ftp://ftp.es.embnet.org/pub/software/emboss/EMBOSS/ \ @@ -16,8 +17,7 @@ DIST_SUBDIR= ${PORTNAME} MAINTAINER= fernan@iib.unsam.edu.ar COMMENT= A collection of contributed EMBOSS applications -BUILD_DEPENDS= ${LOCALBASE}/include/emboss.h:${PORTSDIR}/biology/emboss -LIB_DEPENDS= nucleus.1:${PORTSDIR}/biology/emboss:install +LIB_DEPENDS= nucleus.1:${PORTSDIR}/biology/emboss USE_SUBMAKE= yes USE_GMAKE= yes @@ -30,7 +30,7 @@ OPTIONS= DOMAINATRIX "Protein structure and domain apps" on \ ESIM4 "Align cDNA/EST to genome" on \ HMMER "HMM alignment and searches" on \ MEME "Motif detection" on \ - MSE "Sequence editor" on \ + MSE "A multiple sequence screen editor" on \ PHYLIP "Phylogeny inference" on \ TOPO "Transmembrane display" on @@ -74,6 +74,16 @@ do-extract: fi .endfor +.if !defined(WITHOUT_DOMAINATRIX) +pre-configure:: + @${PATCH} ${PATCH_ARGS} < ${PATCHDIR}/domainatrix-patch-Makefile.in +.endif + +.if !defined(WITHOUT_EMNU) +pre-configure:: + @${PATCH} ${PATCH_ARGS} < ${PATCHDIR}/emnu-patch-Makefile.in +.endif + do-configure: .for app in ${APPLIST} @ cd ${${app}_WRKSRC} && \ diff --git a/biology/embassy/distinfo b/biology/embassy/distinfo index b84869ad3c93..c82f7d7f686f 100644 --- a/biology/embassy/distinfo +++ b/biology/embassy/distinfo @@ -1,16 +1,16 @@ -MD5 (embassy/DOMAINATRIX-1.0.0.tar.gz) = 78e1145851073a277e568ee3a691d999 -SIZE (embassy/DOMAINATRIX-1.0.0.tar.gz) = 551090 -MD5 (embassy/EMNU-1.05.tar.gz) = b091db115506ef89157b1cfb92a964b3 -SIZE (embassy/EMNU-1.05.tar.gz) = 341879 -MD5 (embassy/ESIM4-1.0.0.tar.gz) = 3fa1de555365d79bdc38490e09683632 -SIZE (embassy/ESIM4-1.0.0.tar.gz) = 377821 -MD5 (embassy/HMMER-2.1.1.tar.gz) = e7762beca88f2748cb7449e7f89ca068 -SIZE (embassy/HMMER-2.1.1.tar.gz) = 555504 -MD5 (embassy/MEME-2.3.1.tar.gz) = 014237836443382b767efb4b315c2b6d -SIZE (embassy/MEME-2.3.1.tar.gz) = 417514 -MD5 (embassy/MSE-1.0.0.tar.gz) = f55522c9f474319f56227e6a63c91dad -SIZE (embassy/MSE-1.0.0.tar.gz) = 407726 -MD5 (embassy/PHYLIP-3.57c.tar.gz) = bd242c3382a82d1a842e0a82778a40c2 -SIZE (embassy/PHYLIP-3.57c.tar.gz) = 856814 -MD5 (embassy/TOPO-1.0.0.tar.gz) = 18409cc3ce6a402690b14a73535ebe07 -SIZE (embassy/TOPO-1.0.0.tar.gz) = 345281 +MD5 (embassy/DOMAINATRIX-1.0.0.tar.gz) = 9deff6f5bf526408f0f02c002488ad59 +SIZE (embassy/DOMAINATRIX-1.0.0.tar.gz) = 471604 +MD5 (embassy/EMNU-1.05.tar.gz) = df29ae1e8201081f4413862d7f10edb5 +SIZE (embassy/EMNU-1.05.tar.gz) = 339355 +MD5 (embassy/ESIM4-1.0.0.tar.gz) = 3b8137b3b8ff0e84bc6e1243c7343578 +SIZE (embassy/ESIM4-1.0.0.tar.gz) = 378342 +MD5 (embassy/HMMER-2.1.1.tar.gz) = 56816b26a43c8542f7d12f9069e77843 +SIZE (embassy/HMMER-2.1.1.tar.gz) = 562855 +MD5 (embassy/MEME-2.3.1.tar.gz) = a9fb38886665f3f654da1244c2e1476f +SIZE (embassy/MEME-2.3.1.tar.gz) = 421914 +MD5 (embassy/MSE-1.0.0.tar.gz) = b666681aceb9f07f968585f2edc4a039 +SIZE (embassy/MSE-1.0.0.tar.gz) = 411772 +MD5 (embassy/PHYLIP-3.57c.tar.gz) = 83201895898feb15dbbae6affabd3609 +SIZE (embassy/PHYLIP-3.57c.tar.gz) = 858348 +MD5 (embassy/TOPO-1.0.0.tar.gz) = 0a8fcc84fdba071b20f3046de9fdb487 +SIZE (embassy/TOPO-1.0.0.tar.gz) = 345938 diff --git a/biology/embassy/files/domainatrix-patch-Makefile.in b/biology/embassy/files/domainatrix-patch-Makefile.in new file mode 100644 index 000000000000..d544a23f136b --- /dev/null +++ b/biology/embassy/files/domainatrix-patch-Makefile.in @@ -0,0 +1,11 @@ +--- EMBASSY/DOMAINATRIX-1.0.0/src/Makefile.in.orig Sat May 28 12:21:57 2005 ++++ EMBASSY/DOMAINATRIX-1.0.0/src/Makefile.in Sat May 28 12:22:14 2005 +@@ -315,7 +315,7 @@ + @LOCALLINK_TRUE@ ../../../plplot/libplplot.la \ + @LOCALLINK_TRUE@ $(am__DEPENDENCIES_1) + DEFAULT_INCLUDES = -I. -I$(srcdir) +-depcomp = $(SHELL) $(top_srcdir)/../../depcomp ++depcomp = $(SHELL) $(top_srcdir)/depcomp + am__depfiles_maybe = depfiles + COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \ + $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS) diff --git a/biology/embassy/files/emnu-patch-Makefile.in b/biology/embassy/files/emnu-patch-Makefile.in new file mode 100644 index 000000000000..31688dfd589b --- /dev/null +++ b/biology/embassy/files/emnu-patch-Makefile.in @@ -0,0 +1,11 @@ +--- EMBASSY/EMNU-1.05/source/Makefile.in.orig Sat May 28 12:57:17 2005 ++++ EMBASSY/EMNU-1.05/source/Makefile.in Sat May 28 13:03:33 2005 +@@ -63,7 +63,7 @@ + @LOCALLINK_TRUE@ ../../../plplot/libplplot.la \ + @LOCALLINK_TRUE@ $(am__DEPENDENCIES_1) + DEFAULT_INCLUDES = -I. -I$(srcdir) +-depcomp = $(SHELL) $(top_srcdir)/../../depcomp ++depcomp = $(SHELL) $(top_srcdir)/depcomp + am__depfiles_maybe = depfiles + COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \ + $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS) diff --git a/biology/embassy/pkg-plist b/biology/embassy/pkg-plist index 9f368de07280..22c88962c326 100644 --- a/biology/embassy/pkg-plist +++ b/biology/embassy/pkg-plist @@ -1,29 +1,32 @@ +%%PLIST_DOMAINATRIX%%bin/allversusall +%%PLIST_DOMAINATRIX%%bin/cathparse %%PLIST_DOMAINATRIX%%bin/contacts +%%PLIST_DOMAINATRIX%%bin/domainalign %%PLIST_DOMAINATRIX%%bin/domainer -%%PLIST_DOMAINATRIX%%bin/fraggle +%%PLIST_DOMAINATRIX%%bin/domainnr +%%PLIST_DOMAINATRIX%%bin/domainrep +%%PLIST_DOMAINATRIX%%bin/domainreso +%%PLIST_DOMAINATRIX%%bin/domainseqs +%%PLIST_DOMAINATRIX%%bin/domainsse %%PLIST_DOMAINATRIX%%bin/hetparse -%%PLIST_DOMAINATRIX%%bin/hmmgen %%PLIST_DOMAINATRIX%%bin/interface -%%PLIST_DOMAINATRIX%%bin/libscan +%%PLIST_DOMAINATRIX%%bin/libgen %%PLIST_DOMAINATRIX%%bin/pdbparse %%PLIST_DOMAINATRIX%%bin/pdbplus %%PLIST_DOMAINATRIX%%bin/pdbtosp -%%PLIST_DOMAINATRIX%%bin/profgen +%%PLIST_DOMAINATRIX%%bin/rocon %%PLIST_DOMAINATRIX%%bin/rocplot -%%PLIST_DOMAINATRIX%%bin/scopalign -%%PLIST_DOMAINATRIX%%bin/scopnr %%PLIST_DOMAINATRIX%%bin/scopparse -%%PLIST_DOMAINATRIX%%bin/scoprep -%%PLIST_DOMAINATRIX%%bin/scopreso -%%PLIST_DOMAINATRIX%%bin/scopseqs %%PLIST_DOMAINATRIX%%bin/seqalign +%%PLIST_DOMAINATRIX%%bin/seqfraggle %%PLIST_DOMAINATRIX%%bin/seqnr %%PLIST_DOMAINATRIX%%bin/seqsearch %%PLIST_DOMAINATRIX%%bin/seqsort %%PLIST_DOMAINATRIX%%bin/seqwords %%PLIST_DOMAINATRIX%%bin/siggen -%%PLIST_DOMAINATRIX%%bin/sigplot %%PLIST_DOMAINATRIX%%bin/sigscan +%%PLIST_DOMAINATRIX%%bin/sites +%%PLIST_DOMAINATRIX%%bin/ssematch %%PLIST_EMNU%%bin/emnu %%PLIST_ESIM4%%bin/esim4 %%PLIST_MEME%%bin/meme @@ -76,32 +79,35 @@ %%PLIST_MSE%%lib/libckit.la %%PLIST_MSE%%lib/libckit.a %%PLIST_MSE%%share/EMBOSS/acd/mse.acd +%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/allversusall.acd +%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/cathparse.acd %%PLIST_DOMAINATRIX%%share/EMBOSS/acd/contacts.acd +%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/domainalign.acd %%PLIST_DOMAINATRIX%%share/EMBOSS/acd/domainer.acd -%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/fraggle.acd +%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/domainnr.acd +%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/domainrep.acd +%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/domainreso.acd +%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/domainseqs.acd +%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/domainsse.acd %%PLIST_DOMAINATRIX%%share/EMBOSS/acd/hetparse.acd -%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/hmmgen.acd %%PLIST_DOMAINATRIX%%share/EMBOSS/acd/interface.acd -%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/libscan.acd +%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/libgen.acd %%PLIST_DOMAINATRIX%%share/EMBOSS/acd/pdbparse.acd %%PLIST_DOMAINATRIX%%share/EMBOSS/acd/pdbplus.acd %%PLIST_DOMAINATRIX%%share/EMBOSS/acd/pdbtosp.acd -%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/profgen.acd +%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/rocon.acd %%PLIST_DOMAINATRIX%%share/EMBOSS/acd/rocplot.acd -%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/scopalign.acd -%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/scopnr.acd %%PLIST_DOMAINATRIX%%share/EMBOSS/acd/scopparse.acd -%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/scoprep.acd -%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/scopreso.acd -%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/scopseqs.acd %%PLIST_DOMAINATRIX%%share/EMBOSS/acd/seqalign.acd +%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/seqfraggle.acd %%PLIST_DOMAINATRIX%%share/EMBOSS/acd/seqnr.acd %%PLIST_DOMAINATRIX%%share/EMBOSS/acd/seqsearch.acd %%PLIST_DOMAINATRIX%%share/EMBOSS/acd/seqsort.acd %%PLIST_DOMAINATRIX%%share/EMBOSS/acd/seqwords.acd %%PLIST_DOMAINATRIX%%share/EMBOSS/acd/siggen.acd -%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/sigplot.acd %%PLIST_DOMAINATRIX%%share/EMBOSS/acd/sigscan.acd +%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/sites.acd +%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/ssematch.acd %%PLIST_EMNU%%share/EMBOSS/acd/emnu.acd %%PLIST_ESIM4%%share/EMBOSS/acd/esim4.acd %%PLIST_MEME%%share/EMBOSS/acd/meme.acd @@ -140,5 +146,3 @@ %%PLIST_PHYLIP%%share/EMBOSS/acd/erestml.acd %%PLIST_PHYLIP%%share/EMBOSS/acd/eseqboot.acd %%PLIST_TOPO%%share/EMBOSS/acd/topo.acd -@dirrm share/EMBOSS/acd -@dirrm share/EMBOSS |