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--- archive:bioinformatic_tools:cap3_pcap [2010/04/14 10:23]
galt
+++ archive:bioinformatic_tools:cap3_pcap [2015/07/28 06:22] (current)
ceisenhart ↷ Page moved from bioinformatic_tools:cap3_pcap to archive:bioinformatic_tools:cap3_pcap
@@ Line 27: / Line 27: @@
   wget http://seq.cs.iastate.edu/CAP3/cap3.linux.opteron64.tar
   tar xf cap3.linux.opteron64.tar
-  mv cap3.linux.opteron64.tar CAP3/
+  mv CAP3 cap3
-  cd CAP3
+  mv cap3.linux.opteron64.tar cap3/
+  cd cap3
   cp cap3 ../../bin/
+==== INSTALLING PCAP ====
+  cd /campusdata/BME235/programs
+  wget http://seq.cs.iastate.edu/PCAP/pcap.rep.linux.opteron64.tar
+  tar xf pcap.rep.linux.opteron64.tar
+  mv pcap.rep.linux.opteron64 pcap
+  mv pcap.rep.linux.opteron64.tar pcap/
+  cd pcap
+  cp pcap ../../bin/
+The pcap package has several binaries,
+so we'll have to read the documentation
+and decide what else to copy into bin/
+==== Running PCAP ====
+Actually, we wanted to use autopcap, and so far we have
+been unable to get it to work unless we run it from a sub-directory
+with all the pcap-related programs in ../
+which mimics the structure of their example data. \\
+This is due to the hardwired code in autopcap to access the parent directory where pcap code is saved. The parent directory is used as default.\\
+It took little more than 2 hrs to run the assembly on POG 454 data.\\
 ==== Website ====

Banana Slug Genomics