That document contains the Frequently Asked Questions with Answers to the NCBI toolkit. It is available at ftp://ftp.ncbi.nih.gov/toolbox/FAQ.html In case of any questions don't hesitate to ask us at mailto:toolbox@ncbi.nlm.nih.gov Q. Where can I download the binaries of NCBI toolkit? A. The binaries of NCBI toolkit may be downloaded at: BLAST: ftp://ftp.ncbi.nih.gov/blast/executables/ SEQUIN: ftp://ftp.ncbi.nih.gov/sequin/ FA2HTGS: ftp://ftp.ncbi.nih.gov/fa2htgs/ ENTREZ: ftp://ftp.ncbi.nih.gov/entrez/ CN3D: ftp://ftp.ncbi.nih.gov/cn3d/ Currently NCBI prepares the binaries for the following platforms: IBM -- AIX 4.3.3 DEC Alpha -- OSF1 V5.1 SGI -- IRIX 6.4 SGI -- IRIX 5.3 Sun/Sparc -- Solaris 2.6 Intel x86 -- Solaris 2.7 Intel x86 -- Red Hat Linux release 5.2 with kernel 2.0.36 Intel x86 -- Microsoft NT or Windows 95 (32bit) Motorola 68000 -- MacOS Motorola PowerPC -- MacOS Q. Where can I download the sources of NCBI toolkit? A. The sources of NCBI toolkit for Unix are located at: ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/ncbi.tar.Z The sources of NCBI toolkit for Windows are located at: ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/ncbiz.exe And the sources of NCBI toolkit for Mac are located at: ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/ncbi.hqx Q. How to find the version of the toolkit? A. The source of the ToolKit for Unix, which is located at ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/ncbi.tar.Z should have the file ncbi/VERSION with the date of the building. Q. How to build NCBI toolkit on Unix? A. Read the file ftp://ftp.ncbi.nih.gov/toolbox/readme.unx You should take the sources of NCBI tookit at: ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/ncbi.tar.Z put the archive to the new empty directory: mkdir toolkit cd toolkit #download ncbi.tar.Z here compress -d < ncbi.tar.Z | tar xvf - # the new directory ncbi will be extracted # now run the command: # in sh or bash ./ncbi/make/makedis.csh - 2>&1 | tee out.makedis.csh # in csh or tcsh ./ncbi/make/makedis.csh - |& tee out.makedis.csh The new binaries and libraries will be in ncbi/build subdirectory Q. May I build toolkit on Solaris/Intel or Solaris/Sparc using GNU C? A. Yes, just copy the file ./ncbi/platform/solaris-gcc.ncbi.mk instead of ./ncbi/platform/solarisintel.ncbi.mk (for Solaris/Intel) or ./ncbi/platform/solaris.ncbi.mk (for Solaris/Sparc). Q. How can I build toolkit on Linux with Vibrant library? A. You should purchase Motif for Linux. For example look at: http://www.redhat.com/online_orders.phtml?pid=RH2110 As an alternative to Motif there is free clone which is called Lesstif which can be obtained at http://www.lesstif.org/ We didn't check it work yet, so you can use Lesstif for your own risk. Besides that the X11R6 development toolkit should be installed. Q. How can I build toolkit on Linux without Vibrant library? A. To disable vibrant library you need to edit the files ncbi/platform/linux.ncbi.mk and ncbi/make/makedis.csh to delete all references to: BLIB31=libvibnet.a LIB20=libncbidesk.a LIB28=libvibgif.a LIB30=libncbicn3d.a LIB4=libvibrant.a VIBFLAG="$NCBI_VIBFLAG" VIBLIBS="$NCBI_DISTVIBLIBS" Besides that you should delete the references to Psequin, Nentrez, Cn3D and powblast in ncbi/make/makedis.csh Q. Are there any ready binaries of NCBI toolkit for Debian Linux? A. Yes, they are. Try to look at http://www.pasteur.fr/units/sis/debian/biology-en.html and http://www.debian.org/Packages/unstable/libs/vibrant6.html Q. Can I build threaded version of BLAST on IRIX6.X? A. Yes, you can if you upgrade your system and put the proper patches. SGI recommends the following threads patches on IRIX6 systems: For 6.2 systems, install SG0001404, SG0001645, SG0002000, SG0002420 and SG0002458 (in that order) For 6.3 systems, install SG0001645, SG0002420 and SG0002458 (in that order) For 6.4 systems, install SG0002194, SG0002420 and SG0002458 (in that order) These patches can be obtained by calling SGI customer service or from the web: http://support.sgi.com/ Q. Can I build non-threaded version of BLAST on IRIX6.X? A. Yes, you can. In that case you should specify the flag -DNCBI_NOTHREADS_AVAIL modifying the file ncbi/make/makedis.csh Q. I am having a bit of trouble trying to get the PSI blast to work. The demo program "blastpgp.exe" simple issues an error message saying "cannot open file "nr.pin"" and then crashes. A. That message indicates that it can not find your database 'nr'. After you run formatdb on nr you should have seven files (if you use the '-o T' option) with names: nr.phr nr.pin nr.pnd nr.pni nr.psd nr.psi nr.psq First you should check that all the files are present and if they are not, then look for error messages in formatdb.log. Next check that you are specifying the correct path to the files (or better, run blastpgp.exe in the same directory as the database files). You can also specify the path in your ncbi.ini file by adding: [BLAST] BLASTDB=C:\BLAST\DB where you replace "C:\BLAST\DB" by the directory that contains your BLAST databases. Q. I installed the NCBI Toolkit but when I attempt to run this, I get the error message: FindPath failed A. This error message is usually caused either by not having an ncbi.ini on Windows platforms or the .ncbirc file on UNIx or by not having this file in the proper directory. 1. For UNIX you need to have a .ncbirc file in your home directory which points to the data directories. Example: [NCBI] Data=/home/user/entrez/data 2. For Windows you need to have a ncbi.ini in your WINDOWS or WINNT directory file which points to the data directories. Example: [NCBI] Data=C:\entrez\data 3. For the Mac, the configuration file is called ncbi.cnf, and should be placed in your "System Folder:Preferences" subfolder. Example: [NCBI] Data=MacintoshHD:Entrez Folder:data Q. Can I get a hardcopy of the NCBI Toolkit documentation? A. Yes, we will send you a hardcopy of the toolkit documentation. Please send your request to the NCBI Information help desk at info@ncbi.nlm.nih.gov Include your complete mailing address.