diff options
| -rw-r--r-- | biology/embassy/Makefile | 18 | ||||
| -rw-r--r-- | biology/embassy/distinfo | 102 | ||||
| -rw-r--r-- | biology/embassy/pkg-plist | 37 | ||||
| -rw-r--r-- | biology/emboss/Makefile | 5 | ||||
| -rw-r--r-- | biology/emboss/distinfo | 6 | ||||
| -rw-r--r-- | biology/emboss/pkg-plist | 139 |
6 files changed, 232 insertions, 75 deletions
diff --git a/biology/embassy/Makefile b/biology/embassy/Makefile index fc3d4588c53d..9a4f00bea333 100644 --- a/biology/embassy/Makefile +++ b/biology/embassy/Makefile @@ -7,10 +7,9 @@ # PORTNAME= embassy -PORTVERSION= 6.0.0 -PORTREVISION= 3 +PORTVERSION= 6.2.0 CATEGORIES= biology -MASTER_SITES= ftp://emboss.open-bio.org/pub/EMBOSS/old/${PORTVERSION}/ +MASTER_SITES= ftp://emboss.open-bio.org/pub/EMBOSS/ DIST_SUBDIR= emboss MAINTAINER= fernan@iib.unsam.edu.ar @@ -54,15 +53,15 @@ DOMAINATRIX_VERSION= 0.1.0 EMNU_VERSION= 1.05 ESIM4_VERSION= 1.0.0 HMMER_VERSION= 2.3.2 -MEMENEW_VERSION= 0.1.0 -MSE_VERSION= 1.0.0 -TOPO_VERSION= 1.0.0 -PHYLIPNEW_VERSION= 3.67 +MEMENEW_VERSION= 4.0.0 +MSE_VERSION= 3.0.0 +TOPO_VERSION= 2.0.0 +PHYLIPNEW_VERSION= 3.69 DOMALIGN_VERSION= 0.1.0 DOMSEARCH_VERSION= 0.1.0 SIGNATURE_VERSION= 0.1.0 STRUCTURE_VERSION= 0.1.0 -MYEMBOSS_VERSION= 6.0.0 +MYEMBOSS_VERSION= 6.2.0 VIENNA_VERSION= 1.7.2 MIRA_VERSION= 2.8.2 IPRSCAN_VERSION= 4.3.1 @@ -97,6 +96,9 @@ do-extract: fi .endfor +post-extract: + @${REINPLACE_CMD} -e 's#emboss_doc##g' ${EMBASSY_WRKDIR}/MIRA-2.8.2/Makefile.in + post-patch: @${FIND} ${WRKSRC} -name configure | ${XARGS} ${REINPLACE_CMD} -e 's|echo aout|echo elf|' diff --git a/biology/embassy/distinfo b/biology/embassy/distinfo index d4ab628f009b..564f2279bcc6 100644 --- a/biology/embassy/distinfo +++ b/biology/embassy/distinfo @@ -1,51 +1,51 @@ -MD5 (emboss/DOMAINATRIX-0.1.0.tar.gz) = 0f5211a2ee754b4f32332beaf660964c -SHA256 (emboss/DOMAINATRIX-0.1.0.tar.gz) = 7596e76b79f19d77e27b8ea8a75a3e1ba4c806aa548cb9675f23e2bb434a42b1 -SIZE (emboss/DOMAINATRIX-0.1.0.tar.gz) = 420983 -MD5 (emboss/EMNU-1.05.tar.gz) = df6c267bb12e3ecd19bffe5f678bfdb3 -SHA256 (emboss/EMNU-1.05.tar.gz) = 2f58621cc7151f813ce608dcd5b3505fc84af882c778fe28167508d6851dc333 -SIZE (emboss/EMNU-1.05.tar.gz) = 390229 -MD5 (emboss/ESIM4-1.0.0.tar.gz) = 36d9e1dc37004ff4189f583d8d3b037b -SHA256 (emboss/ESIM4-1.0.0.tar.gz) = 219b3541e2a67d31fd62140c2c9c2b41e2d3d814dec6aaf691f764e337917577 -SIZE (emboss/ESIM4-1.0.0.tar.gz) = 431898 -MD5 (emboss/HMMER-2.3.2.tar.gz) = edc18f5515f1fd712b7d2accf58a9a2e -SHA256 (emboss/HMMER-2.3.2.tar.gz) = 9b27f2b7a9059b017e3bd3d31de08f6fbf7d49c3e025d73abd83ff0567732258 -SIZE (emboss/HMMER-2.3.2.tar.gz) = 565686 -MD5 (emboss/MEMENEW-0.1.0.tar.gz) = 72f4a3b8544aa1603301b7b83692a133 -SHA256 (emboss/MEMENEW-0.1.0.tar.gz) = 5411d1445feb1b5e460e598a9d7e670a4357fe7aa350d96531b1aa9c79fab636 -SIZE (emboss/MEMENEW-0.1.0.tar.gz) = 450102 -MD5 (emboss/MSE-1.0.0.tar.gz) = 3122000020565077a421a53cf114127a -SHA256 (emboss/MSE-1.0.0.tar.gz) = 9e3688ff3514b7ea6cf104fbd2a2e611fe726fb7ac4bebab6f3c103f05c08d90 -SIZE (emboss/MSE-1.0.0.tar.gz) = 445562 -MD5 (emboss/PHYLIPNEW-3.67.tar.gz) = cbd539fb39673cc362d827fa731f03f3 -SHA256 (emboss/PHYLIPNEW-3.67.tar.gz) = efbfdbff0109c62823caf13f20cb6462f54371d55899fcbbe29240e503584945 -SIZE (emboss/PHYLIPNEW-3.67.tar.gz) = 1624802 -MD5 (emboss/TOPO-1.0.0.tar.gz) = 03ea6cf067db1f673ec27195076b0e4a -SHA256 (emboss/TOPO-1.0.0.tar.gz) = a7fd297c5e27becedd4aafd272123a176581c68b90de872fb3cb46356333cc16 -SIZE (emboss/TOPO-1.0.0.tar.gz) = 379929 -MD5 (emboss/DOMALIGN-0.1.0.tar.gz) = 58dff4731762bef6248b163bf2d160bd -SHA256 (emboss/DOMALIGN-0.1.0.tar.gz) = c448dc461b36e299c6338f25c102de2388cc33515eae8fd1dc7097920efa409a -SIZE (emboss/DOMALIGN-0.1.0.tar.gz) = 462156 -MD5 (emboss/DOMSEARCH-0.1.0.tar.gz) = e862f6b4f02f4640f9729862efab5a0a -SHA256 (emboss/DOMSEARCH-0.1.0.tar.gz) = fb34c1b2f668f89abe6912fe75e9828c53802820753aa8a1b952f37894939c95 -SIZE (emboss/DOMSEARCH-0.1.0.tar.gz) = 470537 -MD5 (emboss/SIGNATURE-0.1.0.tar.gz) = cc7c707c41156b6681ddca7b76ff009d -SHA256 (emboss/SIGNATURE-0.1.0.tar.gz) = 0966e165516448e214275e3cafcca91b9bb83d96264d2bf205aace1380138d2f -SIZE (emboss/SIGNATURE-0.1.0.tar.gz) = 574940 -MD5 (emboss/STRUCTURE-0.1.0.tar.gz) = 7df40530fd15f441c531f5dbd5c10fff -SHA256 (emboss/STRUCTURE-0.1.0.tar.gz) = cd8b17947fe764e830bd14887deb85a5f196f490d25b9c6408aaca0c1baecd23 -SIZE (emboss/STRUCTURE-0.1.0.tar.gz) = 532035 -MD5 (emboss/MYEMBOSS-6.0.0.tar.gz) = 5f51d49558131a518ac40220dd7fa0c3 -SHA256 (emboss/MYEMBOSS-6.0.0.tar.gz) = 7f24d800044b0957006c8550de74ca621301f6de1c724980fe90e8a6093b6048 -SIZE (emboss/MYEMBOSS-6.0.0.tar.gz) = 343305 -MD5 (emboss/VIENNA-1.7.2.tar.gz) = f6ec2092de41dafdb6cf302dd5412498 -SHA256 (emboss/VIENNA-1.7.2.tar.gz) = 7bed50f9992aec250f974f5c5fd9a42d49c24f05e0e9fac88bb94b2d76be25db -SIZE (emboss/VIENNA-1.7.2.tar.gz) = 682200 -MD5 (emboss/MIRA-2.8.2.tar.gz) = c74a63e10ce983c39389593693c851e7 -SHA256 (emboss/MIRA-2.8.2.tar.gz) = 33d756bd50fe26c04aff862f34230feaad831cbe538096e4d8e5c8e0b6784fe1 -SIZE (emboss/MIRA-2.8.2.tar.gz) = 365566 -MD5 (emboss/IPRSCAN-4.3.1.tar.gz) = 8164a9b8392d29ba3bc723c1bc5da2ff -SHA256 (emboss/IPRSCAN-4.3.1.tar.gz) = df0bdd33ea6f279ed018f4a22e686cc14ff0e9f65342177b3b9dbb2951c3636a -SIZE (emboss/IPRSCAN-4.3.1.tar.gz) = 339939 -MD5 (emboss/CBSTOOLS-1.0.0.tar.gz) = 9352c924a8c86233fbf6dc80c58cc481 -SHA256 (emboss/CBSTOOLS-1.0.0.tar.gz) = b61b6c19d18dd3a35eef248feb92ee68bcee0e9fc99af5185deee04a17fa3693 -SIZE (emboss/CBSTOOLS-1.0.0.tar.gz) = 343812 +MD5 (emboss/DOMAINATRIX-0.1.0.tar.gz) = fae63eaa478c0864451e969793949499 +SHA256 (emboss/DOMAINATRIX-0.1.0.tar.gz) = 53b1633d8a4fec4335ffe96fff309ef2e61b38140dad916b042522e1a48d5e02 +SIZE (emboss/DOMAINATRIX-0.1.0.tar.gz) = 407290 +MD5 (emboss/EMNU-1.05.tar.gz) = f43feb89e7cf68fe37375a19a2dd971b +SHA256 (emboss/EMNU-1.05.tar.gz) = ccad2f9572b2667b2522e47aa8256b2f17e33a31f74f75991424af0c49ca651d +SIZE (emboss/EMNU-1.05.tar.gz) = 368599 +MD5 (emboss/ESIM4-1.0.0.tar.gz) = 16f732db3f64e702b8030a41f806e50d +SHA256 (emboss/ESIM4-1.0.0.tar.gz) = 8c02b53105f9bb95fd0acda15133ad4ac736e720df93c06ffaa6fe54b9baad10 +SIZE (emboss/ESIM4-1.0.0.tar.gz) = 406757 +MD5 (emboss/HMMER-2.3.2.tar.gz) = e83a34abdcd4ed1419db3b4a1a7bf2ff +SHA256 (emboss/HMMER-2.3.2.tar.gz) = fd60908ffe8fea41259480701d64c3442a6a469945dbe03fdfa5677b1a3dc6a6 +SIZE (emboss/HMMER-2.3.2.tar.gz) = 559938 +MD5 (emboss/MEMENEW-4.0.0.tar.gz) = c9256d7dfebb309533369aecdbe53667 +SHA256 (emboss/MEMENEW-4.0.0.tar.gz) = f5dab1527612e060e6230f579b3243e0da2da086df7ba0e280d0efbb99d5d973 +SIZE (emboss/MEMENEW-4.0.0.tar.gz) = 507901 +MD5 (emboss/MSE-3.0.0.tar.gz) = abb377c097b841308e50a60991ad4b62 +SHA256 (emboss/MSE-3.0.0.tar.gz) = 1fc5f5313cede53ad95122afeb69b4b588f3b564567bff9855a9691b92eea701 +SIZE (emboss/MSE-3.0.0.tar.gz) = 425691 +MD5 (emboss/PHYLIPNEW-3.69.tar.gz) = af08b628e433a0561f830b21412c2969 +SHA256 (emboss/PHYLIPNEW-3.69.tar.gz) = ae0fd57a5b87961d12df8579298d5ec02a147d6678ead4b561dff2c57c5dba67 +SIZE (emboss/PHYLIPNEW-3.69.tar.gz) = 1652212 +MD5 (emboss/TOPO-2.0.0.tar.gz) = 735b6d53e6644b4033ce32f0a2591248 +SHA256 (emboss/TOPO-2.0.0.tar.gz) = 15f1106800ba803e2c5d79dbfa79b5d521e9ed0ca9da0ceaa77e15366613e915 +SIZE (emboss/TOPO-2.0.0.tar.gz) = 377565 +MD5 (emboss/DOMALIGN-0.1.0.tar.gz) = d369817f082da807ca82e8953f04c128 +SHA256 (emboss/DOMALIGN-0.1.0.tar.gz) = 33a12d28c16039663467f34d930b2a0a6ab2ef7d987db94fd8ed4abd02b1bf9f +SIZE (emboss/DOMALIGN-0.1.0.tar.gz) = 430542 +MD5 (emboss/DOMSEARCH-0.1.0.tar.gz) = dd9d7c6be07c254c6d5487aa5678a74a +SHA256 (emboss/DOMSEARCH-0.1.0.tar.gz) = af2e408dcd29b9330df7c310d64c888f53d225ebb0bb5402237891fdcdea7ce3 +SIZE (emboss/DOMSEARCH-0.1.0.tar.gz) = 447445 +MD5 (emboss/SIGNATURE-0.1.0.tar.gz) = 49cfa31d0a42e31e1141cec704bf8ac9 +SHA256 (emboss/SIGNATURE-0.1.0.tar.gz) = e24bda9ff60ef9940f603f4c65b7e5673d6b81ef0c19d53b294197e98bb2497c +SIZE (emboss/SIGNATURE-0.1.0.tar.gz) = 559082 +MD5 (emboss/STRUCTURE-0.1.0.tar.gz) = 6edce4e40a17a6ea836f2e13620c1f86 +SHA256 (emboss/STRUCTURE-0.1.0.tar.gz) = c555e1fc16b377109a1bef21116bfe0907709fb2f629d7cbb4add455bc871050 +SIZE (emboss/STRUCTURE-0.1.0.tar.gz) = 521708 +MD5 (emboss/MYEMBOSS-6.2.0.tar.gz) = f302aafbe22d0f3e1ca6cd4280f91d21 +SHA256 (emboss/MYEMBOSS-6.2.0.tar.gz) = 13edbea0d11a14f67631a4cf6c69985f42c97383d8182f8815e294be03c5ebae +SIZE (emboss/MYEMBOSS-6.2.0.tar.gz) = 322935 +MD5 (emboss/VIENNA-1.7.2.tar.gz) = 90bc38801dfe2d4967ed7b35070856e0 +SHA256 (emboss/VIENNA-1.7.2.tar.gz) = e2288e6a2f4538cce916033208ab12f0ffb8a92bb1d3ab89fae302b785171fb7 +SIZE (emboss/VIENNA-1.7.2.tar.gz) = 649028 +MD5 (emboss/MIRA-2.8.2.tar.gz) = f59b73667f3d212d7dbd43fed6117bd9 +SHA256 (emboss/MIRA-2.8.2.tar.gz) = 9d2a64fdb1b95bb6e2ac280be3352740e9b5f498f2ff17157374a2ca9744601d +SIZE (emboss/MIRA-2.8.2.tar.gz) = 347282 +MD5 (emboss/IPRSCAN-4.3.1.tar.gz) = ac921ebe9555e7f939bd8a06aa524994 +SHA256 (emboss/IPRSCAN-4.3.1.tar.gz) = 179513e2473dc31e5b6153c29670773e7bceaaf84315156961baf8f1e292a289 +SIZE (emboss/IPRSCAN-4.3.1.tar.gz) = 345907 +MD5 (emboss/CBSTOOLS-1.0.0.tar.gz) = c2405d865148cdcfdccdf5623f5fa784 +SHA256 (emboss/CBSTOOLS-1.0.0.tar.gz) = 100131d86d4efeafbd63fc712c82bf493e9d174f0bc505e37bdd35ffb56182ff +SIZE (emboss/CBSTOOLS-1.0.0.tar.gz) = 385340 diff --git a/biology/embassy/pkg-plist b/biology/embassy/pkg-plist index 3badc2e6a7d9..ff9b9963614d 100644 --- a/biology/embassy/pkg-plist +++ b/biology/embassy/pkg-plist @@ -188,14 +188,18 @@ %%PLIST_HMMER%%bin/ehmmsearch %%PLIST_MEMENEW%%share/EMBOSS/acd/emast.acd %%PLIST_MEMENEW%%share/EMBOSS/acd/ememe.acd +%%PLIST_MEMENEW%%share/EMBOSS/acd/ememetext.acd %%PLIST_MEMENEW%%share/EMBOSS/doc/programs/text/emast.txt %%PLIST_MEMENEW%%share/EMBOSS/doc/programs/text/ememe.txt +%%PLIST_MEMENEW%%share/EMBOSS/doc/programs/text/ememetext.txt %%PLIST_MEMENEW%%share/EMBOSS/doc/html/embassy/memenew/index.html %%PLIST_MEMENEW%%share/EMBOSS/doc/html/embassy/memenew/emast.html %%PLIST_MEMENEW%%share/EMBOSS/doc/html/embassy/memenew/ememe.html +%%PLIST_MEMENEW%%share/EMBOSS/doc/html/embassy/memenew/ememetext.html %%PLIST_MEMENEW%%@dirrm share/EMBOSS/doc/html/embassy/memenew %%PLIST_MEMENEW%%bin/emast %%PLIST_MEMENEW%%bin/ememe +%%PLIST_MEMENEW%%bin/ememetext %%PLIST_MSE%%share/EMBOSS/acd/mse.acd %%PLIST_MSE%%share/EMBOSS/doc/programs/text/mse.txt %%PLIST_MSE%%share/EMBOSS/doc/html/embassy/mse/index.html @@ -251,11 +255,14 @@ %%PLIST_PHYLIPNEW%%share/EMBOSS/doc/programs/text/fcontml.txt %%PLIST_PHYLIPNEW%%share/EMBOSS/doc/programs/text/fcontrast.txt %%PLIST_PHYLIPNEW%%share/EMBOSS/doc/programs/text/fdiscboot.txt +%%PLIST_PHYLIPNEW%%share/EMBOSS/doc/programs/text/fdolmove.txt +%%PLIST_PHYLIPNEW%%share/EMBOSS/doc/programs/text/frestdist.txt %%PLIST_PHYLIPNEW%%share/EMBOSS/doc/programs/text/fdnacomp.txt %%PLIST_PHYLIPNEW%%share/EMBOSS/doc/programs/text/fdnadist.txt %%PLIST_PHYLIPNEW%%share/EMBOSS/doc/programs/text/fdnainvar.txt %%PLIST_PHYLIPNEW%%share/EMBOSS/doc/programs/text/fdnaml.txt %%PLIST_PHYLIPNEW%%share/EMBOSS/doc/programs/text/fdnamlk.txt +%%PLIST_PHYLIPNEW%%share/EMBOSS/doc/programs/text/fdnamove.txt %%PLIST_PHYLIPNEW%%share/EMBOSS/doc/programs/text/fdnapars.txt %%PLIST_PHYLIPNEW%%share/EMBOSS/doc/programs/text/fdnapenny.txt %%PLIST_PHYLIPNEW%%share/EMBOSS/doc/programs/text/fdollop.txt @@ -289,6 +296,9 @@ %%PLIST_PHYLIPNEW%%share/EMBOSS/doc/html/embassy/phylipnew/fcontml.html %%PLIST_PHYLIPNEW%%share/EMBOSS/doc/html/embassy/phylipnew/fcontrast.html %%PLIST_PHYLIPNEW%%share/EMBOSS/doc/html/embassy/phylipnew/fdiscboot.html +%%PLIST_PHYLIPNEW%%share/EMBOSS/doc/html/embassy/phylipnew/fdnamove.html +%%PLIST_PHYLIPNEW%%share/EMBOSS/doc/html/embassy/phylipnew/fdolmove.html +%%PLIST_PHYLIPNEW%%share/EMBOSS/doc/html/embassy/phylipnew/frestdist.html %%PLIST_PHYLIPNEW%%share/EMBOSS/doc/html/embassy/phylipnew/fdnacomp.html %%PLIST_PHYLIPNEW%%share/EMBOSS/doc/html/embassy/phylipnew/fdnadist.html %%PLIST_PHYLIPNEW%%share/EMBOSS/doc/html/embassy/phylipnew/fdnainvar.html @@ -374,6 +384,7 @@ %%PLIST_TOPO%%share/EMBOSS/doc/programs/text/topo.txt %%PLIST_TOPO%%share/EMBOSS/doc/html/embassy/topo/index.html %%PLIST_TOPO%%share/EMBOSS/doc/html/embassy/topo/topo.html +%%PLIST_TOPO%%share/EMBOSS/doc/html/embassy/topo/topo.1.topo.gif %%PLIST_TOPO%%@dirrm share/EMBOSS/doc/html/embassy/topo %%PLIST_TOPO%%bin/topo %%PLIST_VIENNA%%share/EMBOSS/acd/vrnaalifold.acd @@ -451,8 +462,34 @@ %%PLIST_MIRA%%share/EMBOSS/acd/emiraest.acd %%PLIST_MIRA%%bin/emira %%PLIST_MIRA%%bin/emiraest +%%PLIST_MYEMBOSS%%share/EMBOSS/doc/html/embassy/myemboss/index.html +%%PLIST_MYEMBOSS%%@dirrm share/EMBOSS/doc/html/embassy/myemboss %%PLIST_IPRSCAN%%share/EMBOSS/acd/eiprscan.acd +%%PLIST_IPRSCAN%%share/EMBOSS/doc/html/embassy/iprscan/eiprscan.html +%%PLIST_IPRSCAN%%share/EMBOSS/doc/html/embassy/iprscan/index.html %%PLIST_IPRSCAN%%bin/eiprscan +%%PLIST_IPRSCAN%%@dirrm share/EMBOSS/doc/html/embassy/iprscan +%%PLIST_CBSTOOLS%%share/EMBOSS/doc/programs/text/elipop.txt +%%PLIST_CBSTOOLS%%share/EMBOSS/doc/programs/text/eiprscan.txt +%%PLIST_CBSTOOLS%%share/EMBOSS/doc/programs/text/echlorop.txt +%%PLIST_CBSTOOLS%%share/EMBOSS/doc/programs/text/enetnglyc.txt +%%PLIST_CBSTOOLS%%share/EMBOSS/doc/programs/text/enetoglyc.txt +%%PLIST_CBSTOOLS%%share/EMBOSS/doc/programs/text/enetphos.txt +%%PLIST_CBSTOOLS%%share/EMBOSS/doc/programs/text/eprop.txt +%%PLIST_CBSTOOLS%%share/EMBOSS/doc/programs/text/esignalp.txt +%%PLIST_CBSTOOLS%%share/EMBOSS/doc/programs/text/etmhmm.txt +%%PLIST_CBSTOOLS%%share/EMBOSS/doc/programs/text/eyinoyang.txt +%%PLIST_CBSTOOLS%%share/EMBOSS/doc/html/embassy/cbstools/index.html +%%PLIST_CBSTOOLS%%share/EMBOSS/doc/html/embassy/cbstools/echlorop.html +%%PLIST_CBSTOOLS%%share/EMBOSS/doc/html/embassy/cbstools/elipop.html +%%PLIST_CBSTOOLS%%share/EMBOSS/doc/html/embassy/cbstools/enetnglyc.html +%%PLIST_CBSTOOLS%%share/EMBOSS/doc/html/embassy/cbstools/enetoglyc.html +%%PLIST_CBSTOOLS%%share/EMBOSS/doc/html/embassy/cbstools/enetphos.html +%%PLIST_CBSTOOLS%%share/EMBOSS/doc/html/embassy/cbstools/eprop.html +%%PLIST_CBSTOOLS%%share/EMBOSS/doc/html/embassy/cbstools/esignalp.html +%%PLIST_CBSTOOLS%%share/EMBOSS/doc/html/embassy/cbstools/etmhmm.html +%%PLIST_CBSTOOLS%%share/EMBOSS/doc/html/embassy/cbstools/eyinoyang.html +%%PLIST_CBSTOOLS%%@dirrm share/EMBOSS/doc/html/embassy/cbstools %%PLIST_CBSTOOLS%%share/EMBOSS/acd/echlorop.acd %%PLIST_CBSTOOLS%%share/EMBOSS/acd/elipop.acd %%PLIST_CBSTOOLS%%share/EMBOSS/acd/enetnglyc.acd diff --git a/biology/emboss/Makefile b/biology/emboss/Makefile index b7e0b08af0e7..2df4733f8a2e 100644 --- a/biology/emboss/Makefile +++ b/biology/emboss/Makefile @@ -6,11 +6,10 @@ # PORTNAME= emboss -PORTVERSION= 6.0.1 -PORTREVISION= 3 +PORTVERSION= 6.2.0 RELEASE= ${PORTNAME:U}-${PORTVERSION} CATEGORIES= biology -MASTER_SITES= ftp://emboss.open-bio.org/pub/EMBOSS/old/${PORTVERSION}/ +MASTER_SITES= ftp://emboss.open-bio.org/pub/EMBOSS/ DISTNAME= ${RELEASE} DIST_SUBDIR= ${PORTNAME} diff --git a/biology/emboss/distinfo b/biology/emboss/distinfo index 760dab2e11e9..2f53731960d5 100644 --- a/biology/emboss/distinfo +++ b/biology/emboss/distinfo @@ -1,3 +1,3 @@ -MD5 (emboss/EMBOSS-6.0.1.tar.gz) = 2182b148dace6bea403deed8facae40d -SHA256 (emboss/EMBOSS-6.0.1.tar.gz) = 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d -SIZE (emboss/EMBOSS-6.0.1.tar.gz) = 20204153 +MD5 (emboss/EMBOSS-6.2.0.tar.gz) = 2e2937dd0493814ca0f64981f4c79319 +SHA256 (emboss/EMBOSS-6.2.0.tar.gz) = 4726371c0bcf3e232a5ee6b334e74b8c284dcbdcb176a475e77699515f8d122b +SIZE (emboss/EMBOSS-6.2.0.tar.gz) = 23430911 diff --git a/biology/emboss/pkg-plist b/biology/emboss/pkg-plist index bc0bb59e818d..aba7ba2a1667 100644 --- a/biology/emboss/pkg-plist +++ b/biology/emboss/pkg-plist @@ -100,6 +100,7 @@ bin/msbar bin/mwcontam bin/mwfilter bin/needle +bin/needleall bin/newcpgreport bin/newcpgseek bin/newseq @@ -109,6 +110,7 @@ bin/nospace bin/notab bin/notseq bin/nthseq +bin/nthseqset bin/octanol bin/oddcomp bin/palindrome @@ -147,11 +149,13 @@ bin/runJemboss.csh bin/seealso bin/seqmatchall bin/seqret +bin/seqretsetall bin/seqretsplit bin/showalign bin/showdb bin/showfeat bin/showorf +bin/showpep bin/showseq bin/shuffleseq bin/sigcleave @@ -161,6 +165,7 @@ bin/sixpack bin/sizeseq bin/skipredundant bin/skipseq +bin/splitsource bin/splitter bin/stretcher bin/stssearch @@ -211,7 +216,6 @@ include/ajfileio.h include/ajfmt.h include/ajgraph.h include/ajgraphstruct.h -include/ajgraphxml.h include/ajhist.h include/ajindex.h include/ajjava.h @@ -237,6 +241,7 @@ include/ajseqread.h include/ajseqtype.h include/ajseqwrite.h include/ajsort.h +include/ajsql.h include/ajstr.h include/ajsys.h include/ajtable.h @@ -245,6 +250,8 @@ include/ajtranslate.h include/ajtree.h include/ajutil.h include/ajvector.h +include/crc32.h +include/deflate.h include/embaln.h include/embcom.h include/embcons.h @@ -271,6 +278,54 @@ include/embread.h include/embshow.h include/embsig.h include/embword.h +include/ensanalysis.h +include/ensassemblyexception.h +include/ensassembly.h +include/ensassemblymapper.h +include/ensattribute.h +include/ensbaseadaptor.h +include/enscache.h +include/enscoordsystem.h +include/ensdatabaseadaptor.h +include/ensdatabaseconnection.h +include/ensdatabaseentry.h +include/ensdata.h +include/ensdensity.h +include/ensditag.h +include/ensembl.h +include/ensexon.h +include/ensexternaldatabase.h +include/ensfeature.h +include/ensgene.h +include/ensgvdata.h +include/ensgvindividual.h +include/ensgvpopulation.h +include/ensgvsample.h +include/ensintron.h +include/enskaryotype.h +include/ensmapper.h +include/ensmarker.h +include/ensmetacoordinate.h +include/ensmetainformation.h +include/ensmiscellaneous.h +include/ensprediction.h +include/ensprojectionsegment.h +include/ensqcalignment.h +include/ensqcdatabase.h +include/ensqc.h +include/ensqcsequence.h +include/ensregistry.h +include/ensrepeat.h +include/ensseqregion.h +include/enssequence.h +include/enssequenceedit.h +include/ensslice.h +include/ensstorable.h +include/enstable.h +include/enstranslation.h +include/enstranscript.h +include/ensutility.h +include/ensvariation.h include/eplplot/disptab.h include/eplplot/drivers.h include/eplplot/metadefs.h @@ -289,25 +344,61 @@ include/eplplot/plstrm.h include/eplplot/plunicode-type1.h include/eplplot/plxwd.h include/eplplot/ps.h +include/expat.h +include/expat_external.h +include/expatemboss.h +include/inffast.h +include/inffixed.h +include/inflate.h +include/inftrees.h include/pcre.h -include/pcre_chartables.c include/pcre_config.h -include/pcre_get.c +include/pcreemboss.h include/pcre_internal.h -include/pcre_printint.c +include/pcre_printint.src include/pcreposix.h +include/trees.h +include/ucp.h +include/zconf.h +include/zlibemboss.h +include/zlib.h +include/zutil.h +lib/libacd.so.6 +lib/libacd.so +lib/libacd.la +lib/libacd.a lib/libajax.a lib/libajax.la lib/libajax.so lib/libajax.so.6 +lib/libajaxdb.a +lib/libajaxdb.la +lib/libajaxdb.so +lib/libajaxdb.so.6 lib/libajaxg.a lib/libajaxg.la lib/libajaxg.so lib/libajaxg.so.6 +lib/libeexpat.a +lib/libeexpat.la +lib/libeexpat.so +lib/libeexpat.so.2 +lib/libensembl.a +lib/libensembl.la +lib/libensembl.so +lib/libensembl.so.6 +lib/libepcre.a +lib/libepcre.la +lib/libepcre.so +lib/libepcre.so.7 lib/libeplplot.a lib/libeplplot.la lib/libeplplot.so lib/libeplplot.so.5 +lib/libezlib.a +lib/libezlib.la +lib/libezlib.so +lib/libezlib.so.2 lib/libnucleus.a lib/libnucleus.la lib/libnucleus.so @@ -317,6 +408,7 @@ lib/libnucleus.so.6 %%DATADIR%%/acd/acdc.acd %%DATADIR%%/acd/acdlog.acd %%DATADIR%%/acd/acdpretty.acd +%%DATADIR%%/acd/acdrelations.acd %%DATADIR%%/acd/acdtable.acd %%DATADIR%%/acd/acdtrace.acd %%DATADIR%%/acd/acdvalid.acd @@ -359,6 +451,7 @@ lib/libnucleus.so.6 %%DATADIR%%/acd/dbxfasta.acd %%DATADIR%%/acd/dbxflat.acd %%DATADIR%%/acd/dbxgcg.acd +%%DATADIR%%/acd/dbxreport.acd %%DATADIR%%/acd/dbxstat.acd %%DATADIR%%/acd/degapseq.acd %%DATADIR%%/acd/density.acd @@ -370,12 +463,14 @@ lib/libnucleus.so.6 %%DATADIR%%/acd/dotpath.acd %%DATADIR%%/acd/dottup.acd %%DATADIR%%/acd/dreg.acd +%%DATADIR%%/acd/edamclean.acd %%DATADIR%%/acd/edialign.acd %%DATADIR%%/acd/einverted.acd %%DATADIR%%/acd/embossdata.acd %%DATADIR%%/acd/embossversion.acd %%DATADIR%%/acd/emma.acd %%DATADIR%%/acd/emowse.acd +%%DATADIR%%/acd/ensembltest.acd %%DATADIR%%/acd/entrails.acd %%DATADIR%%/acd/entret.acd %%DATADIR%%/acd/epestfind.acd @@ -396,13 +491,14 @@ lib/libnucleus.so.6 %%DATADIR%%/acd/garnier.acd %%DATADIR%%/acd/geecee.acd %%DATADIR%%/acd/getorf.acd -%%DATADIR%%/acd/giep.acd %%DATADIR%%/acd/groups.standard %%DATADIR%%/acd/helixturnhelix.acd %%DATADIR%%/acd/histogramtest.acd %%DATADIR%%/acd/hmoment.acd %%DATADIR%%/acd/iep.acd %%DATADIR%%/acd/infoalign.acd +%%DATADIR%%/acd/infobase.acd +%%DATADIR%%/acd/inforesidue.acd %%DATADIR%%/acd/infoseq.acd %%DATADIR%%/acd/intconv.acd %%DATADIR%%/acd/isochore.acd @@ -426,6 +522,7 @@ lib/libnucleus.so.6 %%DATADIR%%/acd/mwcontam.acd %%DATADIR%%/acd/mwfilter.acd %%DATADIR%%/acd/needle.acd +%%DATADIR%%/acd/needleall.acd %%DATADIR%%/acd/newcoils.acd %%DATADIR%%/acd/newcpgreport.acd %%DATADIR%%/acd/newcpgseek.acd @@ -436,6 +533,7 @@ lib/libnucleus.so.6 %%DATADIR%%/acd/notab.acd %%DATADIR%%/acd/notseq.acd %%DATADIR%%/acd/nthseq.acd +%%DATADIR%%/acd/nthseqset.acd %%DATADIR%%/acd/octanol.acd %%DATADIR%%/acd/oddcomp.acd %%DATADIR%%/acd/origsplitter.acd @@ -483,6 +581,7 @@ lib/libnucleus.so.6 %%DATADIR%%/acd/seqretall.acd %%DATADIR%%/acd/seqretallfeat.acd %%DATADIR%%/acd/seqretset.acd +%%DATADIR%%/acd/seqretsetall.acd %%DATADIR%%/acd/seqretsingle.acd %%DATADIR%%/acd/seqretsplit.acd %%DATADIR%%/acd/seqrettype.acd @@ -490,6 +589,7 @@ lib/libnucleus.so.6 %%DATADIR%%/acd/showdb.acd %%DATADIR%%/acd/showfeat.acd %%DATADIR%%/acd/showorf.acd +%%DATADIR%%/acd/showpep.acd %%DATADIR%%/acd/showseq.acd %%DATADIR%%/acd/shuffleseq.acd %%DATADIR%%/acd/sigcleave.acd @@ -499,7 +599,9 @@ lib/libnucleus.so.6 %%DATADIR%%/acd/sizeseq.acd %%DATADIR%%/acd/skipredundant.acd %%DATADIR%%/acd/skipseq.acd +%%DATADIR%%/acd/splitsource.acd %%DATADIR%%/acd/splitter.acd +%%DATADIR%%/acd/sqltest.acd %%DATADIR%%/acd/stretcher.acd %%DATADIR%%/acd/stssearch.acd %%DATADIR%%/acd/supermatcher.acd @@ -516,6 +618,7 @@ lib/libnucleus.so.6 %%DATADIR%%/acd/treetypedisplay.acd %%DATADIR%%/acd/trimest.acd %%DATADIR%%/acd/trimseq.acd +%%DATADIR%%/acd/trimspace.acd %%DATADIR%%/acd/twofeat.acd %%DATADIR%%/acd/union.acd %%DATADIR%%/acd/variables.standard @@ -888,6 +991,7 @@ lib/libnucleus.so.6 %%DATADIR%%/data/Efeatures.gff3protein %%DATADIR%%/data/Efeatures.gffprotein %%DATADIR%%/data/Efeatures.pir +%%DATADIR%%/data/Efeatures.refseqp %%DATADIR%%/data/Efeatures.protein %%DATADIR%%/data/Efeatures.swiss %%DATADIR%%/data/Efreqs.dat @@ -897,9 +1001,13 @@ lib/libnucleus.so.6 %%DATADIR%%/data/Emass.dat %%DATADIR%%/data/Emassmod.dat %%DATADIR%%/data/Ememe.dat +%%DATADIR%%/data/Emethylsites.dat %%DATADIR%%/data/Emolwt.dat %%DATADIR%%/data/Emwfilter.dat %%DATADIR%%/data/Enakai.dat +%%DATADIR%%/data/EnsemblAliases.dat +%%DATADIR%%/data/EnsemblIdentifiers.dat +%%DATADIR%%/data/Etags.gff3protein %%DATADIR%%/data/Epepcoil.dat %%DATADIR%%/data/Epk.dat %%DATADIR%%/data/Epprofile @@ -916,6 +1024,7 @@ lib/libnucleus.so.6 %%DATADIR%%/data/Etags.gffprotein %%DATADIR%%/data/Etags.pir %%DATADIR%%/data/Etags.protein +%%DATADIR%%/data/Etags.refseqp %%DATADIR%%/data/Etags.swiss %%DATADIR%%/data/Etcode.dat %%DATADIR%%/data/Evdw.dat @@ -932,6 +1041,7 @@ lib/libnucleus.so.6 %%DATADIR%%/data/PRINTS/dummyfile %%DATADIR%%/data/PROSITE/dummyfile %%DATADIR%%/data/REBASE/dummyfile +%%DATADIR%%/data/SSSUB %%DATADIR%%/data/edialignmat %%DATADIR%%/data/embossre.equ %%DATADIR%%/data/tp400_dna @@ -1090,6 +1200,7 @@ lib/libnucleus.so.6 %%DOCSDIR%%/programs/html/mwcontam.html %%DOCSDIR%%/programs/html/mwfilter.html %%DOCSDIR%%/programs/html/needle.html +%%DOCSDIR%%/programs/html/needleall.html %%DOCSDIR%%/programs/html/newcpgreport.html %%DOCSDIR%%/programs/html/newcpgseek.html %%DOCSDIR%%/programs/html/newseq.html @@ -1099,6 +1210,7 @@ lib/libnucleus.so.6 %%DOCSDIR%%/programs/html/notab.html %%DOCSDIR%%/programs/html/notseq.html %%DOCSDIR%%/programs/html/nthseq.html +%%DOCSDIR%%/programs/html/nthseqset.html %%DOCSDIR%%/programs/html/nucleic_2d_structure_group.html %%DOCSDIR%%/programs/html/nucleic_codon_usage_group.html %%DOCSDIR%%/programs/html/nucleic_codon_usage_nucleic_gene_finding_group.html @@ -1178,11 +1290,13 @@ lib/libnucleus.so.6 %%DOCSDIR%%/programs/html/seealso.html %%DOCSDIR%%/programs/html/seqmatchall.html %%DOCSDIR%%/programs/html/seqret.html +%%DOCSDIR%%/programs/html/seqretsetall.html %%DOCSDIR%%/programs/html/seqretsplit.html %%DOCSDIR%%/programs/html/showalign.html %%DOCSDIR%%/programs/html/showdb.html %%DOCSDIR%%/programs/html/showfeat.html %%DOCSDIR%%/programs/html/showorf.html +%%DOCSDIR%%/programs/html/showpep.html %%DOCSDIR%%/programs/html/showseq.html %%DOCSDIR%%/programs/html/shuffleseq.html %%DOCSDIR%%/programs/html/sigcleave.html @@ -1192,6 +1306,7 @@ lib/libnucleus.so.6 %%DOCSDIR%%/programs/html/sizeseq.html %%DOCSDIR%%/programs/html/skipredundant.html %%DOCSDIR%%/programs/html/skipseq.html +%%DOCSDIR%%/programs/html/splitsource.html %%DOCSDIR%%/programs/html/splitter.html %%DOCSDIR%%/programs/html/stretcher.html %%DOCSDIR%%/programs/html/stssearch.html @@ -1300,7 +1415,6 @@ lib/libnucleus.so.6 %%DOCSDIR%%/programs/text/featreport.txt %%DOCSDIR%%/programs/text/findkm.txt %%DOCSDIR%%/programs/text/freak.txt -%%DOCSDIR%%/programs/text/frestdist.txt %%DOCSDIR%%/programs/text/fuzznuc.txt %%DOCSDIR%%/programs/text/fuzzpro.txt %%DOCSDIR%%/programs/text/fuzztran.txt @@ -1334,6 +1448,7 @@ lib/libnucleus.so.6 %%DOCSDIR%%/programs/text/mwcontam.txt %%DOCSDIR%%/programs/text/mwfilter.txt %%DOCSDIR%%/programs/text/needle.txt +%%DOCSDIR%%/programs/text/needleall.txt %%DOCSDIR%%/programs/text/newcpgreport.txt %%DOCSDIR%%/programs/text/newcpgseek.txt %%DOCSDIR%%/programs/text/newseq.txt @@ -1343,6 +1458,7 @@ lib/libnucleus.so.6 %%DOCSDIR%%/programs/text/notab.txt %%DOCSDIR%%/programs/text/notseq.txt %%DOCSDIR%%/programs/text/nthseq.txt +%%DOCSDIR%%/programs/text/nthseqset.txt %%DOCSDIR%%/programs/text/octanol.txt %%DOCSDIR%%/programs/text/oddcomp.txt %%DOCSDIR%%/programs/text/palindrome.txt @@ -1380,10 +1496,12 @@ lib/libnucleus.so.6 %%DOCSDIR%%/programs/text/seealso.txt %%DOCSDIR%%/programs/text/seqmatchall.txt %%DOCSDIR%%/programs/text/seqret.txt +%%DOCSDIR%%/programs/text/seqretsetall.txt %%DOCSDIR%%/programs/text/seqretsplit.txt %%DOCSDIR%%/programs/text/showalign.txt %%DOCSDIR%%/programs/text/showdb.txt %%DOCSDIR%%/programs/text/showfeat.txt +%%DOCSDIR%%/programs/text/showpep.txt %%DOCSDIR%%/programs/text/showorf.txt %%DOCSDIR%%/programs/text/showseq.txt %%DOCSDIR%%/programs/text/shuffleseq.txt @@ -1394,6 +1512,7 @@ lib/libnucleus.so.6 %%DOCSDIR%%/programs/text/sizeseq.txt %%DOCSDIR%%/programs/text/skipredundant.txt %%DOCSDIR%%/programs/text/skipseq.txt +%%DOCSDIR%%/programs/text/splitsource.txt %%DOCSDIR%%/programs/text/splitter.txt %%DOCSDIR%%/programs/text/stretcher.txt %%DOCSDIR%%/programs/text/stssearch.txt @@ -1506,7 +1625,6 @@ lib/libnucleus.so.6 %%DATADIR%%/jemboss/images/Job_manager_button.gif %%DATADIR%%/jemboss/images/Refresh_button.gif %%DATADIR%%/jemboss/images/Refresh_button2.gif -%%DATADIR%%/jemboss/lib/JembossPrintAlignment.jar %%DATADIR%%/jemboss/lib/README %%DATADIR%%/jemboss/lib/activation.jar %%DATADIR%%/jemboss/lib/axis/axis-ant.jar @@ -1518,11 +1636,10 @@ lib/libnucleus.so.6 %%DATADIR%%/jemboss/lib/axis/saaj.jar %%DATADIR%%/jemboss/lib/axis/servlet.jar %%DATADIR%%/jemboss/lib/axis/wsdl4j.jar -%%DATADIR%%/jemboss/lib/grout.jar %%DATADIR%%/jemboss/lib/jakarta-regexp-1.2.jar -%%DATADIR%%/jemboss/lib/jalview.jar +%%DATADIR%%/jemboss/lib/jalviewApplet.jar +%%DATADIR%%/jemboss/lib/jemboss.jar %%DATADIR%%/jemboss/lib/mail.jar -%%DATADIR%%/jemboss/lib/xerces.jar %%DATADIR%%/jemboss/org/emboss/jemboss/Jemboss.java %%DATADIR%%/jemboss/org/emboss/jemboss/JembossJarUtil.java %%DATADIR%%/jemboss/org/emboss/jemboss/JembossLogo.java @@ -1667,12 +1784,14 @@ lib/libnucleus.so.6 %%DATADIR%%/jemboss/resources/readme.html %%DATADIR%%/jemboss/resources/readmeAlign.html %%DATADIR%%/jemboss/resources/readmeDNADraw.html +%%DATADIR%%/jemboss/resources/resources.jar %%DATADIR%%/jemboss/resources/results.html %%DATADIR%%/jemboss/resources/seqList.html %%DATADIR%%/jemboss/resources/version %%DATADIR%%/jemboss/runJemboss.sh %%DATADIR%%/jemboss/utils/README %%DATADIR%%/jemboss/utils/install-jemboss-server.sh +%%DATADIR%%/jemboss/utils/jws-launch-button.png %%DATADIR%%/jemboss/utils/keys.sh %%DATADIR%%/jemboss/utils/makeFileManagerJNLP.sh %%DATADIR%%/jemboss/utils/makeJNLP.sh |