This page was last updated on Friday, 30-Jan-2015 09:05:44 CST

Installation notes for CD-HIT version 4.6.1-2012-08-27

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Prerequisites

None

Installation

1. $ ver="v4.6.1-2012-08-27"
2. $ cd /programinstallers/
3. $ wget -N https://cdhit.googlecode.com/files/cd-hit-$ver.tgz
4. $ wget -N http://cdhit.googlecode.com/files/cd-hit-otu-illumina-0.0.1.tar.gz
5. $ wget -N http://cdhit.googlecode.com/files/cd-hit-otu-454-0.0.2-patched.tar.gz
6. $ tar -zxvf cd-hit-$ver.tgz
7. $ cd cd-hit-$ver
8. $ make openmp=yes
9. $ make install

   …
   for prog in cd-hit cd-hit-est cd-hit-2d cd-hit-est-2d cd-hit-div cd-hit-454; do \
   	install -m 0755 $prog /usr/local/bin; \
   done
   install -m 0755 *.pl /usr/local/bin;
   …

10. List of Perl programs that were installed:
    cd-hit-2d-para.pl cd-hit-div.pl cd-hit-para.pl clstr2tree.pl clstr2txt.pl clstr2xml.pl clstr_cut.pl clstr_merge_noorder.pl clstr_merge.pl clstr_quality_eval_by_link.pl clstr_quality_eval.pl clstr_reduce.pl clstr_renumber.pl clstr_rep.pl clstr_reps_faa_rev.pl clstr_rev.pl clstr_select.pl clstr_select_rep.pl clstr_size_histogram.pl clstr_size_stat.pl clstr_sort_by.pl clstr_sort_prot_by.pl clstr_sql_tbl.pl clstr_sql_tbl_sort.pl make_multi_seq.pl plot_2d.pl plot_len1.pl psi-cd-hit-2d-g1.pl psi-cd-hit-2d.pl psi-cd-hit-local.pl psi-cd-hit.pl
11. Copy documentation for web page
    $ mkdir /U:/simonlabweb/bioinformatics/programs/cd-hit
12. $ cp -puv doc/cdhit-user-guide.pdf /U:/simonlabweb/bioinformatics/programs/cd-hit/
13. Cleanup
    $ cd ..
14. $ rm cd-hit-$ver -rf