Ncbi_tools version 20080302 - How to Download and Install on Mac OS X
Monday the 23rd of November, 2009

    ncbi_tools  most recent diff


    version 20080302

      View the most recent changes for the ncbi_tools port at: ncbi_tools.darwinports.com/diff
      Scroll down toward the bottom of the page to get installation instructions for ncbi_tools.
      The raw portfile for ncbi_tools 20080302 is located here:
      http://ncbi_tools.darwinports.com/dports/science/ncbi_tools/Portfile
      Find related portfiles with the unique DarwinPorts.com search feature.
      Check for any related Fink projects here: pdb.finkproject.org/pdb/package.php/ncbi_tools


      The ncbi_tools Portfile 57375 2009-09-10 08:16:41Z ryandesign macports.org $

      PortSystem 1.0

      Name: ncbi_tools
      Version: 20080302
      Description: blast is a set of tools for doing nucleotide and protein searches
      Maintainers: gmail.com:mike.thon
      Category: science
      Platform: darwin
      Homepage: http://www.ncbi.nlm.nih.gov/blast/
      fetch.use_epsv no
      Master Sites: ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools/old/20080302
      distfiles ncbi.tar.gz
      Checksums: md5 f8de9d7264aed7de1d87d2185df2e07c
      dist_subdir ${name}/${version}
      worksrcdir
      use_configure no
      build.cmd './ncbi/make/makedis.csh'
      build.target
      set binaries "Psequin blastall dosimple gil2bin sbtedit asn2ff blastall_old entrcmd idfetch seedtop asn2gb blastcl3 entrez2 impala seqtest asn2idx blastclust errhdr indexpub tbl2asn asn2xml blastpgp fa2htgs makemat test_regexp asndhuff cdscan fastacmd makeset testcore asntool checksub findspl megablast testobj bl2bag.cgi copymat formatdb ncbisort testval bl2seq ddv formatrpsdb nph-viewgif.cgi udv blast debruijn gene2xml psiblast.REAL vecscreen blast.REAL demo_regexp getmesh psiblast_cs.REAL wblast2.REAL blast_cs.REAL demo_regexp_grep getpub rpsblast wblast2_cs.REAL"

      set manpages "Psequin.1 asnval.1 cleanasn.1 formatdb.1 insdseqget.1 tbl2asn.1 asn2all.1 bl2seq.1 copymat.1 formatrpsdb.1 makemat.1 trna2sap.1 asn2asn.1 blast.1 ddv.1 gbseqget.1 makeset.1 trna2tbl.1 asn2ff.1 blastall.1 debruijn.1 gene2xml.1 megablast.1 udv.1 asn2fsa.1 blastall_old.1 entrez2.1 getmesh.1 nps2gps.1 vecscreen.1 asn2gb.1 blastcl3.1 errhdr.1 getpub.1 rpsblast.1 asn2idx.1 blastclust.1 fa2htgs.1 gil2bin.1 sbtedit.1 asn2xml.1 blastpgp.1 fastacmd.1 idfetch.1 seedtop.1 asndhuff.1 cdscan.1 findspl.1 impala.1 sortbyquote.1 asntool.1 checksub.1 fmerge.1 indexpub.1 spidey.1"

      destroot {
      xinstall -m 755 -d ${destroot}${prefix}/share/doc/${name}
      file copy ${worksrcpath}/ncbi/doc ${destroot}${prefix}/share/doc/${name}
      foreach binary ${binaries} {
      xinstall -m 755 ${worksrcpath}/ncbi/bin/${binary} ${destroot}${prefix}/bin/
      }
      foreach manpage ${manpages} {
      xinstall -m 444 ${worksrcpath}/ncbi/doc/man/${manpage} ${destroot}${prefix}/share/man/man1/
      }
      }

      Long Description: ${description}
      livecheck.type regex
      livecheck.url ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools/
      livecheck.regex old/(\[0-9\]+)

    If you haven't already installed Darwin Ports, you can find easy instructions for doing so at the main Darwin Ports page.

    Once Darwin Ports has been installed, in a terminal window and while online, type the following and hit return:


      %  cd /opt/local/bin/portslocation/dports/ncbi_tools
      % sudo port install ncbi_tools
      Password:
    You will then be prompted for your root password, which you should enter. You may have to wait for a few minutes while the software is retrieved from the network and installed for you. Y ou should see something that looks similar to:

      ---> Fetching ncbi_tools
      ---> Verifying checksum for ncbi_tools
      ---> Extracting ncbi_tools
      ---> Configuring ncbi_tools
      ---> Building ncbi_tools with target all
      ---> Staging ncbi_tools into destroot
      ---> Installing ncbi_tools
    - Make sure that you do not close the terminal window while Darwin Ports is working. Once the software has been installed, you can find further information about using ncbi_tools with these commands:
      %  man ncbi_tools
      % apropos ncbi_tools
      % which ncbi_tools
      % locate ncbi_tools

     Where to find more information:

    Darwin Ports



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