Install SPIDER » History » Revision 31
Revision 30 (Amber Herold, 04/27/2012 01:12 PM) → Revision 31/32 (Amber Herold, 11/25/2013 03:56 PM)
h1. Install SPIDER h2. Install documentation at wadsworth.org The Wadsworth Institute provides "detailed documentation":http://www.wadsworth.org/spider_doc/spider/docs/spider-inst-linux.html on how to install SPIDER on various systems. Below we cover _our way_ to get it working on your system. h2. Download SPIDER binary "from wadsworth.org":http://www.wadsworth.org/spider_doc/spider/docs/spi-register.html (250 MiB) bq. Most of our SPIDER scripts were originally designed around SPIDER v14 and v15, but we are diligently working toward compatibility with SPIDER v18. That said you are probably best off using the newest version of SPIDER (v18.10 as of May 2010) and then reporting any bugs to us. h2. Extract the archive <pre>tar -zxvf spiderweb.20.16.tar.gz</pre> spiderweb.18.10.tar.gz</pre> bq. The archive will create 3 folders: spider, spire, and web. At this time only the *spider* program is used within Appion, you can safely ignore web and spire. h2. Install SPIDER * Copy the spider folder to global directory: <pre>sudo mv -v spider /usr/local/</pre> * Next, you need to determine which version of the spider binary you need to use on your system. <pre> cd /usr/local/spider/bin ls spider* spider_linux spider_linux_mp_intel64 spider_linux_mp_opt64 spider_osx_64_pgi spider_linux_mp_intel spider_linux_mpi_opt64 spider_osx_32_pgi </pre> * From the wadsworth.org site: |_. binary file |_. system information | | spider_linux | AMD/Intel 32 (single processor) | | spider_linux_mp_intel | AMD/Intel 32 (multiple processors) | | spider_linux_mp_opt64 | AMD Opteron 64 (multiple processors) | | spider_linux_mp_intel64 | Intel xeon 64 (multiple processors) | | spider_linux_mpi_opt64 | AMD Opteron 64 (for MPI use) | | spider_osx_32_pgi | Intel Apple 32 bit (multiple processors) | | spider_osx_64_pgi | Intel Apple 64 bit (multiple processors) | * Additionally you may run the UNIX file command on an individual program to determine its type <pre> file spider_linux_mp_intel64 spider_linux_mp_intel64: ELF 64-bit LSB executable, AMD x86-64, version 1 (SYSV), for GNU/Linux 2.6.4, statically linked, for GNU/Linux 2.6.4, not stripped </pre> * If you are unsure, use: ** @spider_linux_mp_intel@ for 32bit Intel/AMD systems ** @spider_linux_mp_opt64@ for 64bit Intel/AMD systems * After you determine which spider to use create a link to that file in /usr/local/bin: <pre>sudo ln -sv /usr/local/spider/bin/spider_xxxxx /usr/local/bin/spider</pre> h2. Set environmental variables h3. For @BASH@, create an spider.sh and add the following lines: <pre> export SPIDERDIR=/usr/local/spider export SPMAN_DIR=${SPIDERDIR}/man/ export SPPROC_DIR=${SPIDERDIR}/proc/ export SPBIN_DIR=${SPIDERDIR}/bin/ export PATH=$PATH:${SPIDERDIR}/bin </pre> h3. For @C@ shell, create an spider.csh and add the following lines: <pre> setenv SPIDERDIR /usr/local/spider setenv SPMAN_DIR ${SPIDERDIR}/man/ setenv SPPROC_DIR ${SPIDERDIR}/proc/ setenv SPBIN_DIR ${SPIDERDIR}/bin/ setenv PATH $PATH:${SPIDERDIR}/bin </pre> h3. And then add it to the global /etc/profile.d/ folder <pre> sudo cp -v spider.sh /etc/profile.d/spider.sh sudo chmod 755 /etc/profile.d/spider.sh -or- sudo cp -v spider.csh /etc/profile.d/spider.csh sudo chmod 755 /etc/profile.d/spider.csh </pre> bq. You may need to log out and log back in for these changes to take place. h2. Test SPIDER * Execute the program: ** input: <pre>spider bat/spi</pre> ** output: <pre> \__`O O'__/ SPIDER -- COPYRIGHT ,__xXXXx___ HEALTH RESEARCH INC., ALBANY, NY. __xXXXx__ / /xxx\ \ VERSION: UNIX 18.10 ISSUED: 03/23/2010 / \ DATE: 13-MAY-2010 AT 09:32:42 Results file: results.bat.0 Running: spider .OPERATION:</pre> ** input: <pre>EN D</pre> ** output: <pre> **** SPIDER NORMAL STOP ****</pre> ______ [[Install EMAN|< Install EMAN]] | [[Install Xmipp|Install Xmipp >]] ______