Install SPIDER » History » Version 17
Neil Voss, 05/13/2010 09:14 AM
1 | 1 | Neil Voss | h1. Install SPIDER |
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3 | 12 | Neil Voss | h2. Install documentation at wadsworth.org |
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5 | 14 | Neil Voss | 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 a _our way_ to get it working on your system. |
6 | 12 | Neil Voss | |
7 | 7 | Neil Voss | h2. Download SPIDER binary "from wadsworth.org":http://www.wadsworth.org/spider_doc/spider/docs/spi-register.html (250 MiB) |
8 | 4 | Neil Voss | |
9 | 7 | Neil Voss | 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. |
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11 | 7 | Neil Voss | h2. Extract the archive |
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13 | <pre>tar -zxvf spiderweb.18.10.tar.gz</pre> |
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15 | 9 | Neil Voss | 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. |
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17 | 10 | Neil Voss | h2. Install SPIDER |
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19 | 10 | Neil Voss | * Copy the spider folder to global directory: |
20 | <pre>sudo mv -v spider /usr/local/</pre> |
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21 | 1 | Neil Voss | |
22 | 10 | Neil Voss | * Next, you need to determine which version of the spider binary you need to use on your system. |
23 | 11 | Neil Voss | <pre> |
24 | cd /usr/local/spider/bin |
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25 | ls spider* |
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26 | spider_linux spider_linux_mp_intel64 spider_linux_mp_opt64 spider_osx_64_pgi |
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27 | spider_linux_mp_intel spider_linux_mpi_opt64 spider_osx_32_pgi |
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28 | </pre> |
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29 | 10 | Neil Voss | |
30 | 17 | Neil Voss | * From the wadsworth.org site: |
31 | 16 | Neil Voss | |_. binary file |_. system information | |
32 | | spider_linux | AMD/Intel 32 (single processor) | |
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33 | | spider_linux_mp_intel | AMD/Intel 32 (multiple processors) | |
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34 | | spider_linux_mp_opt64 | AMD Opteron 64 (multiple processors) | |
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35 | | spider_linux_mp_intel64 | Intel xeon 64 (multiple processors) | |
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36 | | spider_linux_mpi_opt64 | AMD Opteron 64 (for MPI use) | |
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37 | | spider_osx_32_pgi | Intel Apple 32 bit (multiple processors) | |
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38 | | spider_osx_64_pgi | Intel Apple 64 bit (multiple processors) | |
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39 | 15 | Neil Voss | |
40 | 17 | Neil Voss | * Additionally you run the UNIX file command on an individual program to determine its type |
41 | <pre> |
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42 | file spider_linux_mp_intel64 |
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43 | 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 |
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44 | </pre> |
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45 | 10 | Neil Voss | |
46 | <pre>sudo ln -sv /usr/local/spider/bin/spider /usr/local/</pre> |
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48 | h2. Set environmental variables |
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50 | h3. For @BASH@, create an spider.sh and add the following lines: |
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52 | 1 | Neil Voss | <pre> |
53 | 10 | Neil Voss | export SPIDER=/usr/local/spider |
54 | export SPMAN_DIR=${SPIDER}/man |
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55 | export SPPROC_DIR=${SPIDER}/proc |
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56 | export SPRGB_DIR=${SPIDER}/rgb |
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57 | 8 | Neil Voss | </pre> |
58 | 1 | Neil Voss | |
59 | 10 | Neil Voss | h3. For @C@ shell, create an spider.csh and add the following lines: |
60 | 1 | Neil Voss | |
61 | <pre> |
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62 | 10 | Neil Voss | setenv SPIDER /usr/local/spider |
63 | setenv SPMAN_DIR ${SPIDER}/man |
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64 | setenv SPPROC_DIR ${SPIDER}/proc |
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65 | setenv SPRGB_DIR ${SPIDER}/rgb |
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66 | 8 | Neil Voss | </pre> |
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68 | h3. And then add it to the global /etc/profile.d/ folder |
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70 | <pre> |
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71 | 10 | Neil Voss | sudo cp -v spider.sh /etc/profile.d/spider.sh |
72 | sudo chmod 755 /etc/profile.d/spider.sh |
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73 | 8 | Neil Voss | |
74 | 10 | Neil Voss | -or- |
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76 | sudo cp -v spider.csh /etc/profile.d/spider.csh |
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77 | sudo chmod 755 /etc/profile.d/spider.csh |
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78 | 1 | Neil Voss | </pre> |
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81 | [[Install EMAN|< Install EMAN]] | [[Install Xmipp|Install Xmipp >]] |