FreeBSD Bugzilla – Attachment 23344 Details for
Bug 40198
Updated port biology/emboss 2.20 -> 2.4.1
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[patch]
file.diff
file.diff (text/plain), 21.71 KB, created by
Tilman Linneweh
on 2002-07-04 21:50:01 UTC
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Description:
file.diff
Filename:
MIME Type:
Creator:
Tilman Linneweh
Created:
2002-07-04 21:50:01 UTC
Size:
21.71 KB
patch
obsolete
>Index: distinfo >=================================================================== >RCS file: /home/ncvs/ports/biology/emboss/distinfo,v >retrieving revision 1.20 >diff -u -r1.20 distinfo >--- distinfo 18 Jan 2002 14:04:03 -0000 1.20 >+++ distinfo 4 Jul 2002 19:54:55 -0000 >@@ -1,7 +1,7 @@ >-MD5 (emboss/EMBOSS-2.2.0.tar.gz) = c6d755f98f558f9f98649c1d1cca44a6 >-MD5 (emboss/EMNU-1.0.5.tar.gz) = 6ba42bfd8484b313f39ef81e03141f66 >-MD5 (emboss/HMMER-2.1.1.tar.gz) = aff42ea8ced9c049f2cc4f84a10efd21 >-MD5 (emboss/MEME-2.3.1.tar.gz) = 92302d22ccb94f9e77c1bb2ca35c0f9c >-MD5 (emboss/MSE-0.0.4.tar.gz) = fdfdb7f4d92f67323b14b7030a1135c9 >-MD5 (emboss/PHYLIP-3.573c.tar.gz) = 5fa81a3cfb4f502c627a30428d49a084 >-MD5 (emboss/TOPO-0.1.tar.gz) = 96fced0b0979157e344fd9b08dc2aa64 >+MD5 (emboss/EMBOSS-2.4.1.tar.gz) = f8e8f053362346d45b696ad6d0ec4aad >+MD5 (emboss/EMNU-1.0.5.tar.gz) = 628f28b24762e75a9546b608cc60f179 >+MD5 (emboss/HMMER-2.1.1.tar.gz) = 1bce29d9f215076c90d2b95b9ba6942f >+MD5 (emboss/MEME-2.3.1.tar.gz) = 6961f0308b122d170a5e8d27f02edbc3 >+MD5 (emboss/MSE-0.0.4.tar.gz) = 067952daa34ce4af71e88d9e87136257 >+MD5 (emboss/PHYLIP-3.573c.tar.gz) = 4e69bc86f429d95f99b5e9d3f83036ab >+MD5 (emboss/TOPO-0.1.tar.gz) = 8ca248a5cf0ad230d3959fbcce013942 >Index: pkg-plist >=================================================================== >RCS file: /home/ncvs/ports/biology/emboss/pkg-plist,v >retrieving revision 1.17 >diff -u -r1.17 pkg-plist >--- pkg-plist 18 Jan 2002 14:04:03 -0000 1.17 >+++ pkg-plist 4 Jul 2002 20:29:46 -0000 >@@ -188,7 +188,6 @@ > bin/preg > bin/prettyplot > bin/prettyseq >-bin/primer3 > bin/primersearch > bin/printsextract > bin/profit >@@ -210,9 +209,6 @@ > bin/seealso > bin/seqmatchall > bin/seqret >-bin/seqretall >-bin/seqretallfeat >-bin/seqretset > bin/seqretsplit > bin/showalign > bin/showdb >@@ -320,6 +316,7 @@ > share/EMBOSS/acd/emowse.acd > share/EMBOSS/acd/entrails.acd > share/EMBOSS/acd/entret.acd >+share/EMBOSS/acd/eprimer3.acd > share/EMBOSS/acd/equicktandem.acd > share/EMBOSS/acd/est2genome.acd > share/EMBOSS/acd/etandem.acd >@@ -339,6 +336,7 @@ > share/EMBOSS/acd/iep.acd > share/EMBOSS/acd/infoalign.acd > share/EMBOSS/acd/infoseq.acd >+share/EMBOSS/acd/interface.acd > share/EMBOSS/acd/isochore.acd > share/EMBOSS/acd/lindna.acd > share/EMBOSS/acd/listor.acd >@@ -365,6 +363,7 @@ > share/EMBOSS/acd/patmatdb.acd > share/EMBOSS/acd/patmatmotifs.acd > share/EMBOSS/acd/patmattest.acd >+share/EMBOSS/acd/pdbtosp.acd > share/EMBOSS/acd/pepcoil.acd > share/EMBOSS/acd/pepinfo.acd > share/EMBOSS/acd/pepnet.acd >@@ -379,7 +378,6 @@ > share/EMBOSS/acd/prettyplot.acd > share/EMBOSS/acd/prettyseq.acd > share/EMBOSS/acd/prima.acd >-share/EMBOSS/acd/primer3.acd > share/EMBOSS/acd/primers.acd > share/EMBOSS/acd/primersearch.acd > share/EMBOSS/acd/printsextract.acd >@@ -397,16 +395,19 @@ > share/EMBOSS/acd/restrict.acd > share/EMBOSS/acd/revseq.acd > share/EMBOSS/acd/scopalign.acd >+share/EMBOSS/acd/scopparse.acd > share/EMBOSS/acd/scope.acd > share/EMBOSS/acd/seealso.acd > share/EMBOSS/acd/seqinfo.acd > share/EMBOSS/acd/seqmatchall.acd >+share/EMBOSS/acd/seqnr.acd > share/EMBOSS/acd/seqret.acd > share/EMBOSS/acd/seqretall.acd > share/EMBOSS/acd/seqretallfeat.acd > share/EMBOSS/acd/seqretset.acd > share/EMBOSS/acd/seqretsingle.acd > share/EMBOSS/acd/seqretsplit.acd >+share/EMBOSS/acd/seqsort.acd > share/EMBOSS/acd/showalign.acd > share/EMBOSS/acd/showdb.acd > share/EMBOSS/acd/showfeat.acd >@@ -429,16 +430,20 @@ > share/EMBOSS/acd/tfm.acd > share/EMBOSS/acd/tfscan.acd > share/EMBOSS/acd/tmap.acd >+share/EMBOSS/acd/tranalign.acd > share/EMBOSS/acd/transeq.acd > share/EMBOSS/acd/treetypedisplay.acd > share/EMBOSS/acd/trimest.acd > share/EMBOSS/acd/trimseq.acd >+share/EMBOSS/acd/union.acd > share/EMBOSS/acd/vectorstrip.acd > share/EMBOSS/acd/water.acd >+share/EMBOSS/acd/whichdb.acd > share/EMBOSS/acd/wobble.acd > share/EMBOSS/acd/wordcount.acd > share/EMBOSS/acd/wordmatch.acd > share/EMBOSS/acd/wossname.acd >+share/EMBOSS/acd/yank.acd > share/EMBOSS/data/CODONS/Eacc.cut > share/EMBOSS/data/CODONS/Eadenovirus5.cut > share/EMBOSS/data/CODONS/Eadenovirus7.cut >@@ -721,6 +726,7 @@ > share/EMBOSS/data/REBASE/dummyfile > share/EMBOSS/data/embossre.equ > share/EMBOSS/emboss.default.template >+share/EMBOSS/jemboss/README > share/EMBOSS/jemboss/LICENSE > share/EMBOSS/jemboss/api/allclasses-frame.html > share/EMBOSS/jemboss/api/deprecated-list.html >@@ -791,79 +797,6 @@ > share/EMBOSS/jemboss/api/packages.html > share/EMBOSS/jemboss/api/serialized-form.html > share/EMBOSS/jemboss/api/stylesheet.css >-share/EMBOSS/jemboss/embreo/LICENSE >-share/EMBOSS/jemboss/embreo/Modules/EmbossSoap.pm >-share/EMBOSS/jemboss/embreo/Modules/EmbreoFile.pm >-share/EMBOSS/jemboss/embreo/Modules/ParseSoapOptions.pm >-share/EMBOSS/jemboss/embreo/Modules/README >-share/EMBOSS/jemboss/embreo/PROBLEMS >-share/EMBOSS/jemboss/embreo/README >-share/EMBOSS/jemboss/embreo/README.macos >-share/EMBOSS/jemboss/embreo/README.properties >-share/EMBOSS/jemboss/embreo/api-docs/allclasses-frame.html >-share/EMBOSS/jemboss/embreo/api-docs/deprecated-list.html >-share/EMBOSS/jemboss/embreo/api-docs/help-doc.html >-share/EMBOSS/jemboss/embreo/api-docs/index-all.html >-share/EMBOSS/jemboss/embreo/api-docs/index.html >-share/EMBOSS/jemboss/embreo/api-docs/overview-tree.html >-share/EMBOSS/jemboss/embreo/api-docs/package-list >-share/EMBOSS/jemboss/embreo/api-docs/serialized-form.html >-share/EMBOSS/jemboss/embreo/api-docs/stylesheet.css >-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoACD.html >-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoAnnotate.html >-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoAppList.html >-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoAuthException.html >-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoAuthPopup.html >-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoAuthPrompt.html >-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoException.html >-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoFrame.html >-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoGroupList.html >-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoGroupTree.html >-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoHelp.html >-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoHelpView.html >-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoJList.html >-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoListFile.html >-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoMakeFileSafe.html >-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoParams.html >-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoPendingResults.html >-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoPrivateRequest.html >-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoPublicRequest.html >-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoResList.html >-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoResListView.html >-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoResSave.html >-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoResView.html >-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoResult.html >-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoRun.html >-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoServiceDesc.html >-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoShowDB.html >-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoStartup.html >-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoTreeCellRenderer.html >-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoUtils.html >-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoFile.html >-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoFileGet.html >-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoFileLaunch.html >-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoFileList.html >-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoFileListView.html >-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoFileMgr.html >-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoFileNode.html >-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoFilePut.html >-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoFileRequest.html >-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoFileRoots.html >-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoFileSave.html >-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoFileTree.html >-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoFileTreePanel.html >-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoFileView.html >-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoFileViewPanel.html >-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoLocalGet.html >-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoLocalRoots.html >-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoLocalTree.html >-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoLocalTreePanel.html >-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoLocalView.html >-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoLocalViewPanel.html >-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/FileNode.html >-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/WindowsAltFileSystemView.html >-share/EMBOSS/jemboss/embreo/cgi-bin/soap.cgi >-share/EMBOSS/jemboss/embreo/embreo-full.jar > share/EMBOSS/jemboss/images/Backward_arrow_button.gif > share/EMBOSS/jemboss/images/Forward_arrow_button.gif > share/EMBOSS/jemboss/images/Go_button.gif >@@ -874,7 +807,6 @@ > share/EMBOSS/jemboss/images/Job_manager_button.gif > share/EMBOSS/jemboss/images/Refresh_button.gif > share/EMBOSS/jemboss/images/Refresh_button2.gif >-share/EMBOSS/jemboss/interface.html > share/EMBOSS/jemboss/lib/README > share/EMBOSS/jemboss/lib/activation.jar > share/EMBOSS/jemboss/lib/jakarta-regexp-1.2.jar >@@ -882,9 +814,13 @@ > share/EMBOSS/jemboss/lib/mail.jar > share/EMBOSS/jemboss/lib/soap.jar > share/EMBOSS/jemboss/lib/xerces.jar >+share/EMBOSS/jemboss/lib/jcert.jar >+share/EMBOSS/jemboss/lib/jnet.jar >+share/EMBOSS/jemboss/lib/jsse.jar > share/EMBOSS/jemboss/org/emboss/jemboss/Jemboss.java > share/EMBOSS/jemboss/org/emboss/jemboss/JembossLogo.java > share/EMBOSS/jemboss/org/emboss/jemboss/JembossParams.java >+share/EMBOSS/jemboss/org/emboss/jemboss/JembossJarUtil.java > share/EMBOSS/jemboss/org/emboss/jemboss/gui/AdvancedOptions.java > share/EMBOSS/jemboss/org/emboss/jemboss/gui/BuildProgramMenu.java > share/EMBOSS/jemboss/org/emboss/jemboss/gui/LaunchJalView.java >@@ -893,6 +829,9 @@ > share/EMBOSS/jemboss/org/emboss/jemboss/gui/ShowResultSet.java > share/EMBOSS/jemboss/org/emboss/jemboss/gui/ShowSavedResults.java > share/EMBOSS/jemboss/org/emboss/jemboss/gui/SwingWorker.java >+share/EMBOSS/jemboss/org/emboss/jemboss/gui/SequenceData.java >+share/EMBOSS/jemboss/org/emboss/jemboss/gui/SequenceList.java >+share/EMBOSS/jemboss/org/emboss/jemboss/gui/MemoryComboBox.java > share/EMBOSS/jemboss/org/emboss/jemboss/gui/filetree/DragTree.java > share/EMBOSS/jemboss/org/emboss/jemboss/gui/filetree/FileEditorDisplay.java > share/EMBOSS/jemboss/org/emboss/jemboss/gui/filetree/FileNode.java >@@ -929,6 +868,8 @@ > share/EMBOSS/jemboss/org/emboss/jemboss/parser/acd/Application.java > share/EMBOSS/jemboss/org/emboss/jemboss/parser/acd/ApplicationFields.java > share/EMBOSS/jemboss/org/emboss/jemboss/parser/acd/ApplicationParam.java >+share/EMBOSS/jemboss/org/emboss/jemboss/parser/AcdVariableResolve.java >+share/EMBOSS/jemboss/org/emboss/jemboss/parser/AjaxUtil.java > share/EMBOSS/jemboss/org/emboss/jemboss/programs/BatchUpdateTimer.java > share/EMBOSS/jemboss/org/emboss/jemboss/programs/JembossProcess.java > share/EMBOSS/jemboss/org/emboss/jemboss/programs/ListFile.java >@@ -936,6 +877,12 @@ > share/EMBOSS/jemboss/org/emboss/jemboss/programs/ResultsUpdateTimer.java > share/EMBOSS/jemboss/org/emboss/jemboss/programs/RunEmbossApplication.java > share/EMBOSS/jemboss/org/emboss/jemboss/server/JembossServer.java >+share/EMBOSS/jemboss/org/emboss/jemboss/server/JembossFileServer.java >+share/EMBOSS/jemboss/org/emboss/jemboss/server/JembossThread.java >+share/EMBOSS/jemboss/org/emboss/jemboss/server/JembossAuthServer.java >+share/EMBOSS/jemboss/org/emboss/jemboss/server/JembossAuthThread.java >+share/EMBOSS/jemboss/org/emboss/jemboss/server/JembossFileAuthServer.java >+share/EMBOSS/jemboss/org/emboss/jemboss/server/TestPublicServer.java > share/EMBOSS/jemboss/org/emboss/jemboss/soap/AuthPopup.java > share/EMBOSS/jemboss/org/emboss/jemboss/soap/CallAjax.java > share/EMBOSS/jemboss/org/emboss/jemboss/soap/GetWossname.java >@@ -943,13 +890,25 @@ > share/EMBOSS/jemboss/org/emboss/jemboss/soap/JembossSoapException.java > share/EMBOSS/jemboss/org/emboss/jemboss/soap/PendingResults.java > share/EMBOSS/jemboss/org/emboss/jemboss/soap/PrivateRequest.java >+share/EMBOSS/jemboss/org/emboss/jemboss/soap/ServerSetup.java >+share/EMBOSS/jemboss/org/emboss/jemboss/soap/FileRoots.java >+share/EMBOSS/jemboss/org/emboss/jemboss/soap/FileList.java >+share/EMBOSS/jemboss/org/emboss/jemboss/soap/PublicRequest.java >+share/EMBOSS/jemboss/org/emboss/jemboss/soap/GetACD.java >+share/EMBOSS/jemboss/org/emboss/jemboss/soap/GetHelp.java >+share/EMBOSS/jemboss/org/emboss/jemboss/soap/ShowDB.java >+share/EMBOSS/jemboss/org/emboss/jemboss/soap/MakeFileSafe.java >+share/EMBOSS/jemboss/utils/install-jemboss-server.sh >+share/EMBOSS/jemboss/utils/keys.sh >+share/EMBOSS/jemboss/utils/makeJNLP.sh >+share/EMBOSS/jemboss/utils/template.html >+share/EMBOSS/jemboss/utils/README >+share/EMBOSS/jemboss/utils/makeJar.csh > share/EMBOSS/jemboss/readme.html > share/EMBOSS/jemboss/resources/jemboss.properties > share/EMBOSS/jemboss/resources/readme.txt > share/EMBOSS/jemboss/resources/version > share/EMBOSS/jemboss/runJemboss.csh >-share/EMBOSS/jemboss/setup.html >-share/EMBOSS/jemboss/utils/makeJar.csh > share/EMBOSS/plstnd5.fnt > share/EMBOSS/plxtnd5.fnt > share/EMBOSS/test/data/aligna.dna >@@ -1005,25 +964,79 @@ > share/EMBOSS/test/data/prot.ncbi > share/EMBOSS/test/data/prot.swiss > share/EMBOSS/test/data/prot.text >+share/EMBOSS/test/data/tranalign.pep >+share/EMBOSS/test/data/tranalign.seq > share/EMBOSS/test/data/z83307.seq > share/EMBOSS/test/embl/acnum.hit > share/EMBOSS/test/embl/acnum.trg >+share/EMBOSS/test/embl/des.hit >+share/EMBOSS/test/embl/des.trg > share/EMBOSS/test/embl/division.lkp > share/EMBOSS/test/embl/entrynam.idx > share/EMBOSS/test/embl/est.dat > share/EMBOSS/test/embl/fun.dat > share/EMBOSS/test/embl/hum1.dat > share/EMBOSS/test/embl/inv.dat >+share/EMBOSS/test/embl/keyword.hit >+share/EMBOSS/test/embl/keyword.trg > share/EMBOSS/test/embl/pln.dat > share/EMBOSS/test/embl/pro.dat > share/EMBOSS/test/embl/rod.dat >+share/EMBOSS/test/embl/seqvn.hit >+share/EMBOSS/test/embl/seqvn.trg > share/EMBOSS/test/embl/sts.dat >+share/EMBOSS/test/embl/taxon.hit >+share/EMBOSS/test/embl/taxon.trg > share/EMBOSS/test/embl/vrl.dat > share/EMBOSS/test/embl/vrt.dat >+share/EMBOSS/test/genbank/acnum.hit >+share/EMBOSS/test/genbank/acnum.trg >+share/EMBOSS/test/genbank/division.lkp >+share/EMBOSS/test/genbank/entrynam.idx >+share/EMBOSS/test/genbank/seqvn.hit >+share/EMBOSS/test/genbank/seqvn.trg >+share/EMBOSS/test/genbank/des.hit >+share/EMBOSS/test/genbank/des.trg >+share/EMBOSS/test/genbank/keyword.hit >+share/EMBOSS/test/genbank/keyword.trg >+share/EMBOSS/test/genbank/taxon.hit >+share/EMBOSS/test/genbank/taxon.trg >+share/EMBOSS/test/genbank/gbbct1.seq >+share/EMBOSS/test/genbank/gbest1.seq >+share/EMBOSS/test/genbank/gbinv1.seq >+share/EMBOSS/test/genbank/gbpln1.seq >+share/EMBOSS/test/genbank/gbpln2.seq >+share/EMBOSS/test/genbank/gbpri1.seq >+share/EMBOSS/test/genbank/gbrod1.seq >+share/EMBOSS/test/genbank/gbsts1.seq >+share/EMBOSS/test/genbank/gbvrl1.seq >+share/EMBOSS/test/genbank/gbvrt.seq >+share/EMBOSS/test/gb/acnum.hit >+share/EMBOSS/test/gb/acnum.trg >+share/EMBOSS/test/gb/division.lkp >+share/EMBOSS/test/gb/entrynam.idx >+share/EMBOSS/test/gb/seqvn.hit >+share/EMBOSS/test/gb/seqvn.trg >+share/EMBOSS/test/gb/des.hit >+share/EMBOSS/test/gb/des.trg >+share/EMBOSS/test/gb/keyword.hit >+share/EMBOSS/test/gb/keyword.trg >+share/EMBOSS/test/gb/taxon.hit >+share/EMBOSS/test/gb/taxon.trg >+share/EMBOSS/test/gb/ba.ref >+share/EMBOSS/test/gb/ba.seq >+share/EMBOSS/test/gb/htg.ref >+share/EMBOSS/test/gb/htg.seq > share/EMBOSS/test/pir/acnum.hit > share/EMBOSS/test/pir/acnum.trg >+share/EMBOSS/test/pir/des.hit >+share/EMBOSS/test/pir/des.trg > share/EMBOSS/test/pir/division.lkp > share/EMBOSS/test/pir/entrynam.idx >+share/EMBOSS/test/pir/keyword.hit >+share/EMBOSS/test/pir/keyword.trg >+share/EMBOSS/test/pir/taxon.hit >+share/EMBOSS/test/pir/taxon.trg > share/EMBOSS/test/pir/pir1.header > share/EMBOSS/test/pir/pir1.names > share/EMBOSS/test/pir/pir1.numbers >@@ -1053,6 +1066,14 @@ > share/EMBOSS/test/swiss/division.lkp > share/EMBOSS/test/swiss/entrynam.idx > share/EMBOSS/test/swiss/seq.dat >+share/EMBOSS/test/swiss/seqvn.hit >+share/EMBOSS/test/swiss/seqvn.trg >+share/EMBOSS/test/swiss/des.hit >+share/EMBOSS/test/swiss/des.trg >+share/EMBOSS/test/swiss/keyword.hit >+share/EMBOSS/test/swiss/keyword.trg >+share/EMBOSS/test/swiss/taxon.hit >+share/EMBOSS/test/swiss/taxon.trg > share/EMBOSS/test/swnew/acnum.hit > share/EMBOSS/test/swnew/acnum.trg > share/EMBOSS/test/swnew/division.lkp >@@ -1060,11 +1081,21 @@ > share/EMBOSS/test/swnew/new_seq.dat > share/EMBOSS/test/swnew/upd_ann.dat > share/EMBOSS/test/swnew/upd_seq.dat >+share/EMBOSS/test/swnew/seqvn.hit >+share/EMBOSS/test/swnew/seqvn.trg >+share/EMBOSS/test/swnew/des.hit >+share/EMBOSS/test/swnew/des.trg >+share/EMBOSS/test/swnew/keyword.hit >+share/EMBOSS/test/swnew/keyword.trg >+share/EMBOSS/test/swnew/taxon.hit >+share/EMBOSS/test/swnew/taxon.trg > share/EMBOSS/test/wormpep/acnum.hit > share/EMBOSS/test/wormpep/acnum.trg > share/EMBOSS/test/wormpep/division.lkp > share/EMBOSS/test/wormpep/entrynam.idx > share/EMBOSS/test/wormpep/wormpep >+share/EMBOSS/test/wormpep/des.hit >+share/EMBOSS/test/wormpep/des.trg > share/doc/EMBOSS/manuals/EMBOSS-FreeBSD-HOWTO.txt > share/doc/EMBOSS/manuals/admin.aux > share/doc/EMBOSS/manuals/admin.dvi >@@ -1272,8 +1303,6 @@ > share/doc/EMBOSS/programs/html/prettyplot3.gif > share/doc/EMBOSS/programs/html/prettyplot4.gif > share/doc/EMBOSS/programs/html/prettyseq.html >-share/doc/EMBOSS/programs/html/prima.html >-share/doc/EMBOSS/programs/html/primer3.html > share/doc/EMBOSS/programs/html/primersearch.html > share/doc/EMBOSS/programs/html/printsextract.html > share/doc/EMBOSS/programs/html/profit.html >@@ -1350,6 +1379,20 @@ > share/doc/EMBOSS/programs/html/wordcount.html > share/doc/EMBOSS/programs/html/wordmatch.html > share/doc/EMBOSS/programs/html/wossname.html >+share/doc/EMBOSS/programs/html/pdbtosp.html >+share/doc/EMBOSS/programs/html/psiblasts.html >+share/doc/EMBOSS/programs/html/scopparse.html >+share/doc/EMBOSS/programs/html/seqnr.html >+share/doc/EMBOSS/programs/html/seqsort.html >+share/doc/EMBOSS/programs/html/tranalign.html >+share/doc/EMBOSS/programs/html/union.html >+share/doc/EMBOSS/programs/html/whichdb.html >+share/doc/EMBOSS/programs/html/yank.html >+share/doc/EMBOSS/programs/html/alignwrap.html >+share/doc/EMBOSS/programs/html/dichet.html >+share/doc/EMBOSS/programs/html/eprimer3.html >+share/doc/EMBOSS/programs/html/interface.html >+share/doc/EMBOSS/programs/html/jembossctl.html > share/doc/EMBOSS/programs/text/SITE-DIRECTED.txt > share/doc/EMBOSS/programs/text/abiview.txt > share/doc/EMBOSS/programs/text/ajtest.txt >@@ -1497,8 +1540,6 @@ > share/doc/EMBOSS/programs/text/preg.txt > share/doc/EMBOSS/programs/text/prettyplot.txt > share/doc/EMBOSS/programs/text/prettyseq.txt >-share/doc/EMBOSS/programs/text/prima.txt >-share/doc/EMBOSS/programs/text/primer3.txt > share/doc/EMBOSS/programs/text/primersearch.txt > share/doc/EMBOSS/programs/text/printsextract.txt > share/doc/EMBOSS/programs/text/profit.txt >@@ -1559,6 +1600,20 @@ > share/doc/EMBOSS/programs/text/wordcount.txt > share/doc/EMBOSS/programs/text/wordmatch.txt > share/doc/EMBOSS/programs/text/wossname.txt >+share/doc/EMBOSS/programs/text/jembossctl.txt >+share/doc/EMBOSS/programs/text/pdbtosp.txt >+share/doc/EMBOSS/programs/text/psiblasts.txt >+share/doc/EMBOSS/programs/text/scopparse.txt >+share/doc/EMBOSS/programs/text/seqnr.txt >+share/doc/EMBOSS/programs/text/seqsort.txt >+share/doc/EMBOSS/programs/text/tranalign.txt >+share/doc/EMBOSS/programs/text/union.txt >+share/doc/EMBOSS/programs/text/whichdb.txt >+share/doc/EMBOSS/programs/text/yank.txt >+share/doc/EMBOSS/programs/text/alignwrap.txt >+share/doc/EMBOSS/programs/text/dichet.txt >+share/doc/EMBOSS/programs/text/eprimer3.txt >+share/doc/EMBOSS/programs/text/interface.txt > share/doc/EMBOSS/tutorials/biblio.bib > share/doc/EMBOSS/tutorials/dottup.ps.gz > share/doc/EMBOSS/tutorials/emboss-gcg.ppt >@@ -1580,6 +1635,8 @@ > @dirrm share/EMBOSS/test/swnew > @dirrm share/EMBOSS/test/swiss > @dirrm share/EMBOSS/test/pir >+@dirrm share/EMBOSS/test/genbank >+@dirrm share/EMBOSS/test/gb > @dirrm share/EMBOSS/test/embl > @dirrm share/EMBOSS/test/data > @dirrm share/EMBOSS/test >@@ -1600,16 +1657,6 @@ > @dirrm share/EMBOSS/jemboss/org > @dirrm share/EMBOSS/jemboss/lib > @dirrm share/EMBOSS/jemboss/images >-@dirrm share/EMBOSS/jemboss/embreo/cgi-bin >-@dirrm share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr >-@dirrm share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo >-@dirrm share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp >-@dirrm share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc >-@dirrm share/EMBOSS/jemboss/embreo/api-docs/uk/ac >-@dirrm share/EMBOSS/jemboss/embreo/api-docs/uk >-@dirrm share/EMBOSS/jemboss/embreo/api-docs >-@dirrm share/EMBOSS/jemboss/embreo/Modules >-@dirrm share/EMBOSS/jemboss/embreo > @dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss/soap > @dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss/programs > @dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss/parser/acd >cvs diff: Diffing files
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