Install dependencies

This pipeline requires:

  • HMMER3.1
  • mothur
  • RDP mcclust
  • python pandas, numpy, scipy, matplotlib, and screed package.

This tutorial is made on a 64 bit linux (ubuntu) machine. If you have 32 bit machine, the installer file links needs to be changed for HMMER3.1 and mothur.

HMMER3.0 or lower does not work due to change in HMM format (.hmm).

setup installation directory


In [34]:
cd ~/Desktop/SSUsearch/


/home/gjr/Desktop/SSUsearch

In [35]:
mkdir -p ./external_tools

In [36]:
cd ./external_tools


/home/gjr/Desktop/SSUsearch/external_tools

In [37]:
mkdir -p ./bin

Install HMMER


In [4]:
!wget -c http://selab.janelia.org/software/hmmer3/3.1b1/hmmer-3.1b1-linux-intel-x86_64.tar.gz -O hmmer-3.1b1-linux-intel-x86_64.tar.gz


--2015-10-25 07:37:28--  http://selab.janelia.org/software/hmmer3/3.1b1/hmmer-3.1b1-linux-intel-x86_64.tar.gz
Resolving selab.janelia.org (selab.janelia.org)... 206.241.0.22
Connecting to selab.janelia.org (selab.janelia.org)|206.241.0.22|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 20174637 (19M) [application/x-gzip]
Saving to: `hmmer-3.1b1-linux-intel-x86_64.tar.gz'

100%[======================================>] 20,174,637  2.18M/s   in 9.0s    

2015-10-25 07:37:37 (2.14 MB/s) - `hmmer-3.1b1-linux-intel-x86_64.tar.gz' saved [20174637/20174637]


In [5]:
!tar -xzvf hmmer-3.1b1-linux-intel-x86_64.tar.gz


hmmer-3.1b1-linux-intel-x86_64/
hmmer-3.1b1-linux-intel-x86_64/lib/
hmmer-3.1b1-linux-intel-x86_64/lib/libhmmer.a
hmmer-3.1b1-linux-intel-x86_64/install-sh
hmmer-3.1b1-linux-intel-x86_64/documentation/
hmmer-3.1b1-linux-intel-x86_64/documentation/Makefile.in
hmmer-3.1b1-linux-intel-x86_64/documentation/man/
hmmer-3.1b1-linux-intel-x86_64/documentation/man/hmmbuild.man
hmmer-3.1b1-linux-intel-x86_64/documentation/man/boilerplate-tail
hmmer-3.1b1-linux-intel-x86_64/documentation/man/hmmer.man
hmmer-3.1b1-linux-intel-x86_64/documentation/man/phmmer.man
hmmer-3.1b1-linux-intel-x86_64/documentation/man/hmmpgmd.man
hmmer-3.1b1-linux-intel-x86_64/documentation/man/hmmalign.man
hmmer-3.1b1-linux-intel-x86_64/documentation/man/hmmconvert.man
hmmer-3.1b1-linux-intel-x86_64/documentation/man/nhmmer.man
hmmer-3.1b1-linux-intel-x86_64/documentation/man/hmmscan.man
hmmer-3.1b1-linux-intel-x86_64/documentation/man/hmmpress.man
hmmer-3.1b1-linux-intel-x86_64/documentation/man/hmmemit.man
hmmer-3.1b1-linux-intel-x86_64/documentation/man/Makefile.in
hmmer-3.1b1-linux-intel-x86_64/documentation/man/hmmfetch.man
hmmer-3.1b1-linux-intel-x86_64/documentation/man/nhmmscan.man
hmmer-3.1b1-linux-intel-x86_64/documentation/man/hmmstat.man
hmmer-3.1b1-linux-intel-x86_64/documentation/man/hmmsearch.man
hmmer-3.1b1-linux-intel-x86_64/documentation/man/jackhmmer.man
hmmer-3.1b1-linux-intel-x86_64/documentation/man/hmmsim.man
hmmer-3.1b1-linux-intel-x86_64/documentation/man/alimask.man
hmmer-3.1b1-linux-intel-x86_64/config.sub
hmmer-3.1b1-linux-intel-x86_64/binaries/
hmmer-3.1b1-linux-intel-x86_64/binaries/esl-ssdraw
hmmer-3.1b1-linux-intel-x86_64/binaries/nhmmscan
hmmer-3.1b1-linux-intel-x86_64/binaries/esl-alipid
hmmer-3.1b1-linux-intel-x86_64/binaries/hmmpress
hmmer-3.1b1-linux-intel-x86_64/binaries/esl-construct
hmmer-3.1b1-linux-intel-x86_64/binaries/esl-compalign
hmmer-3.1b1-linux-intel-x86_64/binaries/hmmsim
hmmer-3.1b1-linux-intel-x86_64/binaries/esl-sfetch
hmmer-3.1b1-linux-intel-x86_64/binaries/hmmsearch
hmmer-3.1b1-linux-intel-x86_64/binaries/esl-mask
hmmer-3.1b1-linux-intel-x86_64/binaries/esl-compstruct
hmmer-3.1b1-linux-intel-x86_64/binaries/esl-histplot
hmmer-3.1b1-linux-intel-x86_64/binaries/hmmfetch
hmmer-3.1b1-linux-intel-x86_64/binaries/hmmstat
hmmer-3.1b1-linux-intel-x86_64/binaries/esl-selectn
hmmer-3.1b1-linux-intel-x86_64/binaries/nhmmer
hmmer-3.1b1-linux-intel-x86_64/binaries/esl-cluster
hmmer-3.1b1-linux-intel-x86_64/binaries/hmmscan
hmmer-3.1b1-linux-intel-x86_64/binaries/esl-alistat
hmmer-3.1b1-linux-intel-x86_64/binaries/hmmbuild
hmmer-3.1b1-linux-intel-x86_64/binaries/hmmalign
hmmer-3.1b1-linux-intel-x86_64/binaries/esl-reformat
hmmer-3.1b1-linux-intel-x86_64/binaries/esl-alimap
hmmer-3.1b1-linux-intel-x86_64/binaries/esl-seqrange
hmmer-3.1b1-linux-intel-x86_64/binaries/alimask
hmmer-3.1b1-linux-intel-x86_64/binaries/hmmc2
hmmer-3.1b1-linux-intel-x86_64/binaries/hmmlogo
hmmer-3.1b1-linux-intel-x86_64/binaries/esl-alimask
hmmer-3.1b1-linux-intel-x86_64/binaries/jackhmmer
hmmer-3.1b1-linux-intel-x86_64/binaries/phmmer
hmmer-3.1b1-linux-intel-x86_64/binaries/esl-alimanip
hmmer-3.1b1-linux-intel-x86_64/binaries/esl-shuffle
hmmer-3.1b1-linux-intel-x86_64/binaries/hmmconvert
hmmer-3.1b1-linux-intel-x86_64/binaries/esl-afetch
hmmer-3.1b1-linux-intel-x86_64/binaries/hmmemit
hmmer-3.1b1-linux-intel-x86_64/binaries/esl-alimerge
hmmer-3.1b1-linux-intel-x86_64/binaries/esl-weight
hmmer-3.1b1-linux-intel-x86_64/binaries/esl-seqstat
hmmer-3.1b1-linux-intel-x86_64/binaries/esl-stranslate
hmmer-3.1b1-linux-intel-x86_64/binaries/hmmpgmd
hmmer-3.1b1-linux-intel-x86_64/LICENSE
hmmer-3.1b1-linux-intel-x86_64/configure
hmmer-3.1b1-linux-intel-x86_64/INSTALL
hmmer-3.1b1-linux-intel-x86_64/configure.ac
hmmer-3.1b1-linux-intel-x86_64/include/
hmmer-3.1b1-linux-intel-x86_64/include/p7_gmxb.h
hmmer-3.1b1-linux-intel-x86_64/include/p7_hmmcache.h
hmmer-3.1b1-linux-intel-x86_64/include/p7_gbands.h
hmmer-3.1b1-linux-intel-x86_64/include/impl_sse.h
hmmer-3.1b1-linux-intel-x86_64/include/cachedb.h
hmmer-3.1b1-linux-intel-x86_64/include/p7_gmxchk.h
hmmer-3.1b1-linux-intel-x86_64/include/p7_config.h
hmmer-3.1b1-linux-intel-x86_64/include/hmmer.h
hmmer-3.1b1-linux-intel-x86_64/RELEASE-NOTES
hmmer-3.1b1-linux-intel-x86_64/Userguide.pdf
hmmer-3.1b1-linux-intel-x86_64/README
hmmer-3.1b1-linux-intel-x86_64/Makefile.in
hmmer-3.1b1-linux-intel-x86_64/profmark/
hmmer-3.1b1-linux-intel-x86_64/profmark/x-fps-ncbiblast+
hmmer-3.1b1-linux-intel-x86_64/profmark/x-hmmsearch-max
hmmer-3.1b1-linux-intel-x86_64/profmark/x-fps-ncbiblast
hmmer-3.1b1-linux-intel-x86_64/profmark/x-phmmer-consensus
hmmer-3.1b1-linux-intel-x86_64/profmark/x-fps-ssearch
hmmer-3.1b1-linux-intel-x86_64/profmark/x-h2-ls
hmmer-3.1b1-linux-intel-x86_64/profmark/x-single-ssearch
hmmer-3.1b1-linux-intel-x86_64/profmark/x-iterate-psiblast
hmmer-3.1b1-linux-intel-x86_64/profmark/x-single-phmmer
hmmer-3.1b1-linux-intel-x86_64/profmark/pmark.param
hmmer-3.1b1-linux-intel-x86_64/profmark/x-fps-wublast
hmmer-3.1b1-linux-intel-x86_64/profmark/x-single-ncbiblast
hmmer-3.1b1-linux-intel-x86_64/profmark/x-fps-fasta
hmmer-3.1b1-linux-intel-x86_64/profmark/Makefile.in
hmmer-3.1b1-linux-intel-x86_64/profmark/pmark-master.pl
hmmer-3.1b1-linux-intel-x86_64/profmark/x-hmmsearch
hmmer-3.1b1-linux-intel-x86_64/profmark/x-fps-phmmer
hmmer-3.1b1-linux-intel-x86_64/profmark/x-psiblast
hmmer-3.1b1-linux-intel-x86_64/profmark/x-psiblast+
hmmer-3.1b1-linux-intel-x86_64/profmark/rocplot.pl
hmmer-3.1b1-linux-intel-x86_64/profmark/x-sam
hmmer-3.1b1-linux-intel-x86_64/profmark/x-h2-fs
hmmer-3.1b1-linux-intel-x86_64/profmark/create-profmark.c
hmmer-3.1b1-linux-intel-x86_64/profmark/rocplot.c
hmmer-3.1b1-linux-intel-x86_64/profmark/00README
hmmer-3.1b1-linux-intel-x86_64/profmark/x-iterate-jackhmmer
hmmer-3.1b1-linux-intel-x86_64/aclocal.m4
hmmer-3.1b1-linux-intel-x86_64/src/
hmmer-3.1b1-linux-intel-x86_64/src/p7_hmmwindow.c
hmmer-3.1b1-linux-intel-x86_64/src/evalues.c
hmmer-3.1b1-linux-intel-x86_64/src/generic_decoding.c
hmmer-3.1b1-linux-intel-x86_64/src/generic_optacc.c
hmmer-3.1b1-linux-intel-x86_64/src/mpisupport.c
hmmer-3.1b1-linux-intel-x86_64/src/p7_prior.c
hmmer-3.1b1-linux-intel-x86_64/src/p7_tophits.c
hmmer-3.1b1-linux-intel-x86_64/src/p7_gmxb.h
hmmer-3.1b1-linux-intel-x86_64/src/impl_sse/
hmmer-3.1b1-linux-intel-x86_64/src/impl_sse/mpi.c
hmmer-3.1b1-linux-intel-x86_64/src/impl_sse/00MANIFEST
hmmer-3.1b1-linux-intel-x86_64/src/impl_sse/msvfilter.c
hmmer-3.1b1-linux-intel-x86_64/src/impl_sse/optacc.c
hmmer-3.1b1-linux-intel-x86_64/src/impl_sse/impl_sse.h
hmmer-3.1b1-linux-intel-x86_64/src/impl_sse/decoding.c
hmmer-3.1b1-linux-intel-x86_64/src/impl_sse/vitfilter.c
hmmer-3.1b1-linux-intel-x86_64/src/impl_sse/Makefile.in
hmmer-3.1b1-linux-intel-x86_64/src/impl_sse/fwdback.c
hmmer-3.1b1-linux-intel-x86_64/src/impl_sse/null2.c
hmmer-3.1b1-linux-intel-x86_64/src/impl_sse/ssvfilter.c
hmmer-3.1b1-linux-intel-x86_64/src/impl_sse/stotrace.c
hmmer-3.1b1-linux-intel-x86_64/src/impl_sse/vitscore.c
hmmer-3.1b1-linux-intel-x86_64/src/impl_sse/p7_oprofile.c
hmmer-3.1b1-linux-intel-x86_64/src/impl_sse/fbparsers.tex
hmmer-3.1b1-linux-intel-x86_64/src/impl_sse/io.c
hmmer-3.1b1-linux-intel-x86_64/src/impl_sse/p7_omx.ai
hmmer-3.1b1-linux-intel-x86_64/src/impl_sse/p7_omx.c
hmmer-3.1b1-linux-intel-x86_64/src/generic_vtrace.c
hmmer-3.1b1-linux-intel-x86_64/src/nhmmer.c
hmmer-3.1b1-linux-intel-x86_64/src/p7_spensemble.c
hmmer-3.1b1-linux-intel-x86_64/src/p7_builder.c
hmmer-3.1b1-linux-intel-x86_64/src/generic_viterbi.c
hmmer-3.1b1-linux-intel-x86_64/src/p7_hmmcache.h
hmmer-3.1b1-linux-intel-x86_64/src/hmmalign.c
hmmer-3.1b1-linux-intel-x86_64/src/p7_gbands.h
hmmer-3.1b1-linux-intel-x86_64/src/modelconfig.c
hmmer-3.1b1-linux-intel-x86_64/src/p7_scoredata.c
hmmer-3.1b1-linux-intel-x86_64/src/hmmdmstr.c
hmmer-3.1b1-linux-intel-x86_64/src/generic_fwdback_rescaled.c
hmmer-3.1b1-linux-intel-x86_64/src/jackhmmer.c
hmmer-3.1b1-linux-intel-x86_64/src/phmmer.c
hmmer-3.1b1-linux-intel-x86_64/src/p7_alidisplay.c
hmmer-3.1b1-linux-intel-x86_64/src/generic_null2.c
hmmer-3.1b1-linux-intel-x86_64/src/logsum.c
hmmer-3.1b1-linux-intel-x86_64/src/p7_hmmcache.c
hmmer-3.1b1-linux-intel-x86_64/src/p7_gmxchk.c
hmmer-3.1b1-linux-intel-x86_64/src/impl_vmx/
hmmer-3.1b1-linux-intel-x86_64/src/impl_vmx/mpi.c
hmmer-3.1b1-linux-intel-x86_64/src/impl_vmx/00MANIFEST
hmmer-3.1b1-linux-intel-x86_64/src/impl_vmx/impl_vmx.h
hmmer-3.1b1-linux-intel-x86_64/src/impl_vmx/msvfilter.c
hmmer-3.1b1-linux-intel-x86_64/src/impl_vmx/optacc.c
hmmer-3.1b1-linux-intel-x86_64/src/impl_vmx/decoding.c
hmmer-3.1b1-linux-intel-x86_64/src/impl_vmx/vitfilter.c
hmmer-3.1b1-linux-intel-x86_64/src/impl_vmx/Makefile.in
hmmer-3.1b1-linux-intel-x86_64/src/impl_vmx/fwdback.c
hmmer-3.1b1-linux-intel-x86_64/src/impl_vmx/null2.c
hmmer-3.1b1-linux-intel-x86_64/src/impl_vmx/stotrace.c
hmmer-3.1b1-linux-intel-x86_64/src/impl_vmx/vitscore.c
hmmer-3.1b1-linux-intel-x86_64/src/impl_vmx/p7_oprofile.c
hmmer-3.1b1-linux-intel-x86_64/src/impl_vmx/io.c
hmmer-3.1b1-linux-intel-x86_64/src/impl_vmx/p7_omx.c
hmmer-3.1b1-linux-intel-x86_64/src/p7_hmm.c
hmmer-3.1b1-linux-intel-x86_64/src/hmmscan.c
hmmer-3.1b1-linux-intel-x86_64/src/cachedb.h
hmmer-3.1b1-linux-intel-x86_64/src/hmmdutils.c
hmmer-3.1b1-linux-intel-x86_64/src/p7_gmxchk.h
hmmer-3.1b1-linux-intel-x86_64/src/seqmodel.c
hmmer-3.1b1-linux-intel-x86_64/src/itest_brute.c
hmmer-3.1b1-linux-intel-x86_64/src/hmmer.c
hmmer-3.1b1-linux-intel-x86_64/src/p7_null3.c
hmmer-3.1b1-linux-intel-x86_64/src/nhmmscan.c
hmmer-3.1b1-linux-intel-x86_64/src/generic_fwdback.c
hmmer-3.1b1-linux-intel-x86_64/src/generic_fwdback_banded.c
hmmer-3.1b1-linux-intel-x86_64/src/p7_gmx.c
hmmer-3.1b1-linux-intel-x86_64/src/Makefile.in
hmmer-3.1b1-linux-intel-x86_64/src/hmmsim.c
hmmer-3.1b1-linux-intel-x86_64/src/hmmpress.itest.pl
hmmer-3.1b1-linux-intel-x86_64/src/hmmconvert.c
hmmer-3.1b1-linux-intel-x86_64/src/modelstats.c
hmmer-3.1b1-linux-intel-x86_64/src/hmmstat.c
hmmer-3.1b1-linux-intel-x86_64/src/p7_domaindef.c
hmmer-3.1b1-linux-intel-x86_64/src/errors.c
hmmer-3.1b1-linux-intel-x86_64/src/eweight.c
hmmer-3.1b1-linux-intel-x86_64/src/hmmbuild.c
hmmer-3.1b1-linux-intel-x86_64/src/generic_msv.c
hmmer-3.1b1-linux-intel-x86_64/src/p7_gbands.c
hmmer-3.1b1-linux-intel-x86_64/src/hmmc2.c
hmmer-3.1b1-linux-intel-x86_64/src/alimask.c
hmmer-3.1b1-linux-intel-x86_64/src/p7_profile.c
hmmer-3.1b1-linux-intel-x86_64/src/generic_fwdback_chk.c
hmmer-3.1b1-linux-intel-x86_64/src/hmmsearch.c
hmmer-3.1b1-linux-intel-x86_64/src/p7_gmxb.c
hmmer-3.1b1-linux-intel-x86_64/src/impl_dummy/
hmmer-3.1b1-linux-intel-x86_64/src/impl_dummy/mpi.c
hmmer-3.1b1-linux-intel-x86_64/src/impl_dummy/impl_dummy.h
hmmer-3.1b1-linux-intel-x86_64/src/impl_dummy/msvfilter.c
hmmer-3.1b1-linux-intel-x86_64/src/impl_dummy/optacc.c
hmmer-3.1b1-linux-intel-x86_64/src/impl_dummy/decoding.c
hmmer-3.1b1-linux-intel-x86_64/src/impl_dummy/vitfilter.c
hmmer-3.1b1-linux-intel-x86_64/src/impl_dummy/Makefile.in
hmmer-3.1b1-linux-intel-x86_64/src/impl_dummy/fwdback.c
hmmer-3.1b1-linux-intel-x86_64/src/impl_dummy/null2.c
hmmer-3.1b1-linux-intel-x86_64/src/impl_dummy/stotrace.c
hmmer-3.1b1-linux-intel-x86_64/src/impl_dummy/vitscore.c
hmmer-3.1b1-linux-intel-x86_64/src/impl_dummy/p7_oprofile.c
hmmer-3.1b1-linux-intel-x86_64/src/impl_dummy/io.c
hmmer-3.1b1-linux-intel-x86_64/src/impl_dummy/p7_omx.c
hmmer-3.1b1-linux-intel-x86_64/src/hmmpgmd_client_example.pl
hmmer-3.1b1-linux-intel-x86_64/src/hmmlogo.c
hmmer-3.1b1-linux-intel-x86_64/src/p7_pipeline.c
hmmer-3.1b1-linux-intel-x86_64/src/hmmpress.c
hmmer-3.1b1-linux-intel-x86_64/src/tracealign.c
hmmer-3.1b1-linux-intel-x86_64/src/h2_io.c
hmmer-3.1b1-linux-intel-x86_64/src/hmmfetch.c
hmmer-3.1b1-linux-intel-x86_64/src/hmmdwrkr.c
hmmer-3.1b1-linux-intel-x86_64/src/hmmpgmd.c
hmmer-3.1b1-linux-intel-x86_64/src/p7_trace.c
hmmer-3.1b1-linux-intel-x86_64/src/p7_config.h.in
hmmer-3.1b1-linux-intel-x86_64/src/heatmap.c
hmmer-3.1b1-linux-intel-x86_64/src/p7_bg.c
hmmer-3.1b1-linux-intel-x86_64/src/hmmemit.c
hmmer-3.1b1-linux-intel-x86_64/src/generic_stotrace.c
hmmer-3.1b1-linux-intel-x86_64/src/hmmpgmd.h
hmmer-3.1b1-linux-intel-x86_64/src/cachedb.c
hmmer-3.1b1-linux-intel-x86_64/src/hmmer.h
hmmer-3.1b1-linux-intel-x86_64/src/build.c
hmmer-3.1b1-linux-intel-x86_64/src/emit.c
hmmer-3.1b1-linux-intel-x86_64/src/hmmpgmd2msa.c
hmmer-3.1b1-linux-intel-x86_64/src/p7_hmmfile.c
hmmer-3.1b1-linux-intel-x86_64/share/
hmmer-3.1b1-linux-intel-x86_64/share/doc/
hmmer-3.1b1-linux-intel-x86_64/share/doc/hmmer/
hmmer-3.1b1-linux-intel-x86_64/share/man/
hmmer-3.1b1-linux-intel-x86_64/share/man/man1/
hmmer-3.1b1-linux-intel-x86_64/share/man/man1/phmmer.1
hmmer-3.1b1-linux-intel-x86_64/share/man/man1/jackhmmer.1
hmmer-3.1b1-linux-intel-x86_64/share/man/man1/hmmsim.1
hmmer-3.1b1-linux-intel-x86_64/share/man/man1/hmmemit.1
hmmer-3.1b1-linux-intel-x86_64/share/man/man1/hmmscan.1
hmmer-3.1b1-linux-intel-x86_64/share/man/man1/hmmalign.1
hmmer-3.1b1-linux-intel-x86_64/share/man/man1/hmmfetch.1
hmmer-3.1b1-linux-intel-x86_64/share/man/man1/hmmer.1
hmmer-3.1b1-linux-intel-x86_64/share/man/man1/hmmpgmd.1
hmmer-3.1b1-linux-intel-x86_64/share/man/man1/hmmconvert.1
hmmer-3.1b1-linux-intel-x86_64/share/man/man1/nhmmscan.1
hmmer-3.1b1-linux-intel-x86_64/share/man/man1/hmmsearch.1
hmmer-3.1b1-linux-intel-x86_64/share/man/man1/hmmpress.1
hmmer-3.1b1-linux-intel-x86_64/share/man/man1/alimask.1
hmmer-3.1b1-linux-intel-x86_64/share/man/man1/hmmbuild.1
hmmer-3.1b1-linux-intel-x86_64/share/man/man1/nhmmer.1
hmmer-3.1b1-linux-intel-x86_64/share/man/man1/hmmstat.1
hmmer-3.1b1-linux-intel-x86_64/testsuite/
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hmmer-3.1b1-linux-intel-x86_64/easel/esl_msa_testfiles/selex/
hmmer-3.1b1-linux-intel-x86_64/easel/esl_msa_testfiles/selex/selex.bad.11
hmmer-3.1b1-linux-intel-x86_64/easel/esl_msa_testfiles/selex/00MANIFEST
hmmer-3.1b1-linux-intel-x86_64/easel/esl_msa_testfiles/selex/selex.bad.12
hmmer-3.1b1-linux-intel-x86_64/easel/esl_msa_testfiles/selex/selex.good.1
hmmer-3.1b1-linux-intel-x86_64/easel/esl_msa_testfiles/selex/selex.bad.14
hmmer-3.1b1-linux-intel-x86_64/easel/esl_msa_testfiles/selex/selex.bad.10
hmmer-3.1b1-linux-intel-x86_64/easel/esl_msa_testfiles/selex/selex.bad.2
hmmer-3.1b1-linux-intel-x86_64/easel/esl_msa_testfiles/selex/selex.good.2
hmmer-3.1b1-linux-intel-x86_64/easel/esl_msa_testfiles/selex/selex.bad.9
hmmer-3.1b1-linux-intel-x86_64/easel/esl_msa_testfiles/selex/selex.bad.5
hmmer-3.1b1-linux-intel-x86_64/easel/esl_msa_testfiles/selex/selex.bad.6
hmmer-3.1b1-linux-intel-x86_64/easel/esl_msa_testfiles/selex/selex.bad.7
hmmer-3.1b1-linux-intel-x86_64/easel/esl_msa_testfiles/selex/selex.bad.1
hmmer-3.1b1-linux-intel-x86_64/easel/esl_msa_testfiles/selex/selex.bad.3
hmmer-3.1b1-linux-intel-x86_64/easel/esl_msa_testfiles/selex/selex.good.3
hmmer-3.1b1-linux-intel-x86_64/easel/esl_msa_testfiles/selex/selex.bad.4
hmmer-3.1b1-linux-intel-x86_64/easel/esl_msa_testfiles/selex/selex.bad.8
hmmer-3.1b1-linux-intel-x86_64/easel/esl_msa_testfiles/selex/selex.bad.13
hmmer-3.1b1-linux-intel-x86_64/easel/esl_rootfinder.h
hmmer-3.1b1-linux-intel-x86_64/easel/testsuite/
hmmer-3.1b1-linux-intel-x86_64/easel/testsuite/driver_report.pl
hmmer-3.1b1-linux-intel-x86_64/easel/testsuite/e2.sh
hmmer-3.1b1-linux-intel-x86_64/easel/testsuite/valgrind_report.pl
hmmer-3.1b1-linux-intel-x86_64/easel/testsuite/coverage_report.pl
hmmer-3.1b1-linux-intel-x86_64/easel/testsuite/trna-5.stk
hmmer-3.1b1-linux-intel-x86_64/easel/testsuite/i3-blank-gf.pl
hmmer-3.1b1-linux-intel-x86_64/easel/testsuite/Makefile.in
hmmer-3.1b1-linux-intel-x86_64/easel/testsuite/i1-degen-residues.pl
hmmer-3.1b1-linux-intel-x86_64/easel/testsuite/testsuite.sqc
hmmer-3.1b1-linux-intel-x86_64/easel/testsuite/i2-ncbi-indices.pl
hmmer-3.1b1-linux-intel-x86_64/easel/testsuite/trna-ssdraw.ps
hmmer-3.1b1-linux-intel-x86_64/easel/esl_ssi.tex
hmmer-3.1b1-linux-intel-x86_64/easel/esl_sse.h
hmmer-3.1b1-linux-intel-x86_64/easel/esl_normal.tex
hmmer-3.1b1-linux-intel-x86_64/easel/esl_rootfinder.tex
hmmer-3.1b1-linux-intel-x86_64/easel/esl_ratematrix.tex
hmmer-3.1b1-linux-intel-x86_64/easel/config.guess
hmmer-3.1b1-linux-intel-x86_64/easel/esl_gev.h
hmmer-3.1b1-linux-intel-x86_64/easel/esl_sqio_ascii.c
hmmer-3.1b1-linux-intel-x86_64/easel/esl_distance.c
hmmer-3.1b1-linux-intel-x86_64/easel/esl_histogram.c
hmmer-3.1b1-linux-intel-x86_64/easel/esl_dmatrix.h
hmmer-3.1b1-linux-intel-x86_64/easel/demotic/
hmmer-3.1b1-linux-intel-x86_64/easel/demotic/blast2profmark
hmmer-3.1b1-linux-intel-x86_64/easel/demotic/demotic_blast.pm
hmmer-3.1b1-linux-intel-x86_64/easel/demotic/fasta2profmark
hmmer-3.1b1-linux-intel-x86_64/easel/demotic/regress/
hmmer-3.1b1-linux-intel-x86_64/easel/demotic/regress/ncbi-blastp-tbl.out
hmmer-3.1b1-linux-intel-x86_64/easel/demotic/regress/wu-blastp-tbl.out
hmmer-3.1b1-linux-intel-x86_64/easel/demotic/regress/ssearch-profmark.out
hmmer-3.1b1-linux-intel-x86_64/easel/demotic/regress/ncbi-blastp-profmark.out
hmmer-3.1b1-linux-intel-x86_64/easel/demotic/regress/hmmsearch-tbl.out
hmmer-3.1b1-linux-intel-x86_64/easel/demotic/regress/psiblast-tbl.out
hmmer-3.1b1-linux-intel-x86_64/easel/demotic/regress/fasta-tbl.out
hmmer-3.1b1-linux-intel-x86_64/easel/demotic/regress/h2-tbl.out
hmmer-3.1b1-linux-intel-x86_64/easel/demotic/regress/psiblast-profmark.out
hmmer-3.1b1-linux-intel-x86_64/easel/demotic/regress/phmmer-profmark.out
hmmer-3.1b1-linux-intel-x86_64/easel/demotic/regress/hmmsearch-profmark.out
hmmer-3.1b1-linux-intel-x86_64/easel/demotic/regress/fasta-profmark.out
hmmer-3.1b1-linux-intel-x86_64/easel/demotic/regress/phmmer-tbl.out
hmmer-3.1b1-linux-intel-x86_64/easel/demotic/regress/wu-blastp-profmark.out
hmmer-3.1b1-linux-intel-x86_64/easel/demotic/regress/h2-profmark.out
hmmer-3.1b1-linux-intel-x86_64/easel/demotic/regress/ssearch-tbl.out
hmmer-3.1b1-linux-intel-x86_64/easel/demotic/h22tbl
hmmer-3.1b1-linux-intel-x86_64/easel/demotic/h22profmark
hmmer-3.1b1-linux-intel-x86_64/easel/demotic/hmmer2tbl
hmmer-3.1b1-linux-intel-x86_64/easel/demotic/test.pl
hmmer-3.1b1-linux-intel-x86_64/easel/demotic/hmmer2profmark
hmmer-3.1b1-linux-intel-x86_64/easel/demotic/examples/
hmmer-3.1b1-linux-intel-x86_64/easel/demotic/examples/example.wu-blastp.out
hmmer-3.1b1-linux-intel-x86_64/easel/demotic/examples/example.psiblast.out
hmmer-3.1b1-linux-intel-x86_64/easel/demotic/examples/example.phmmer.out
hmmer-3.1b1-linux-intel-x86_64/easel/demotic/examples/example-single.fa.pin
hmmer-3.1b1-linux-intel-x86_64/easel/demotic/examples/example-single.fa.psq
hmmer-3.1b1-linux-intel-x86_64/easel/demotic/examples/example-single.asnt
hmmer-3.1b1-linux-intel-x86_64/easel/demotic/examples/example-single.sto
hmmer-3.1b1-linux-intel-x86_64/easel/demotic/examples/example.h2.out
hmmer-3.1b1-linux-intel-x86_64/easel/demotic/examples/example-single.pbl
hmmer-3.1b1-linux-intel-x86_64/easel/demotic/examples/example.sto
hmmer-3.1b1-linux-intel-x86_64/easel/demotic/examples/example.ncbi-blastp.out
hmmer-3.1b1-linux-intel-x86_64/easel/demotic/examples/example-single.fa.phr
hmmer-3.1b1-linux-intel-x86_64/easel/demotic/examples/example-single.fa
hmmer-3.1b1-linux-intel-x86_64/easel/demotic/examples/example.ssearch.out
hmmer-3.1b1-linux-intel-x86_64/easel/demotic/examples/example.fa
hmmer-3.1b1-linux-intel-x86_64/easel/demotic/examples/example-single-psiquery.fa
hmmer-3.1b1-linux-intel-x86_64/easel/demotic/examples/example.hmm2
hmmer-3.1b1-linux-intel-x86_64/easel/demotic/examples/example.hmmsearch.out
hmmer-3.1b1-linux-intel-x86_64/easel/demotic/examples/example.fasta.out
hmmer-3.1b1-linux-intel-x86_64/easel/demotic/examples/example.hmm
hmmer-3.1b1-linux-intel-x86_64/easel/demotic/infernal_tab2gff.pl
hmmer-3.1b1-linux-intel-x86_64/easel/demotic/demotic_h2.pm
hmmer-3.1b1-linux-intel-x86_64/easel/demotic/demotic_hmmer.pm
hmmer-3.1b1-linux-intel-x86_64/easel/demotic/fasta2tbl
hmmer-3.1b1-linux-intel-x86_64/easel/demotic/blast2tbl
hmmer-3.1b1-linux-intel-x86_64/easel/demotic/demotic_infernal_tab.pm
hmmer-3.1b1-linux-intel-x86_64/easel/demotic/demotic_fasta.pm
hmmer-3.1b1-linux-intel-x86_64/easel/demotic/00README
hmmer-3.1b1-linux-intel-x86_64/easel/esl_sqio_ncbi.c
hmmer-3.1b1-linux-intel-x86_64/easel/easel.h
hmmer-3.1b1-linux-intel-x86_64/easel/esl_threads.h
hmmer-3.1b1-linux-intel-x86_64/easel/esl_ratematrix.h
hmmer-3.1b1-linux-intel-x86_64/easel/esl_gev.tex
hmmer-3.1b1-linux-intel-x86_64/easel/esl_msa.tex
hmmer-3.1b1-linux-intel-x86_64/easel/esl_sse.c
hmmer-3.1b1-linux-intel-x86_64/easel/esl_stretchexp.h
hmmer-3.1b1-linux-intel-x86_64/easel/COPYRIGHT
hmmer-3.1b1-linux-intel-x86_64/easel/esl_msafile_clustal.h
hmmer-3.1b1-linux-intel-x86_64/easel/esl_keyhash.h
hmmer-3.1b1-linux-intel-x86_64/easel/esl_exponential.tex
hmmer-3.1b1-linux-intel-x86_64/easel/esl_composition.h
hmmer-3.1b1-linux-intel-x86_64/easel/esl_vectorops.tex
hmmer-3.1b1-linux-intel-x86_64/easel/esl_msafile_clustal.c
hmmer-3.1b1-linux-intel-x86_64/easel/esl_scorematrix.tex
hmmer-3.1b1-linux-intel-x86_64/easel/esl_keyhash.tex
hmmer-3.1b1-linux-intel-x86_64/easel/interface_lapack.c
hmmer-3.1b1-linux-intel-x86_64/easel/esl_hmm.c
hmmer-3.1b1-linux-intel-x86_64/easel/esl_msafile.c
hmmer-3.1b1-linux-intel-x86_64/easel/esl_stopwatch.tex
hmmer-3.1b1-linux-intel-x86_64/easel/esl_weibull.tex
hmmer-3.1b1-linux-intel-x86_64/easel/esl_ssi.c
hmmer-3.1b1-linux-intel-x86_64/easel/esl_mixgev.h
hmmer-3.1b1-linux-intel-x86_64/easel/esl_tree.h
hmmer-3.1b1-linux-intel-x86_64/easel/esl_vmx.h
hmmer-3.1b1-linux-intel-x86_64/easel/esl_msa.c
hmmer-3.1b1-linux-intel-x86_64/easel/esl_mem.c
hmmer-3.1b1-linux-intel-x86_64/easel/esl_dirichlet.h
hmmer-3.1b1-linux-intel-x86_64/easel/esl_msaweight.h
hmmer-3.1b1-linux-intel-x86_64/easel/esl_minimizer.tex
hmmer-3.1b1-linux-intel-x86_64/easel/esl_mpi.h
hmmer-3.1b1-linux-intel-x86_64/easel/00README
hmmer-3.1b1-linux-intel-x86_64/easel/formats/
hmmer-3.1b1-linux-intel-x86_64/easel/formats/genbank.bad.1
hmmer-3.1b1-linux-intel-x86_64/easel/formats/stockholm.1
hmmer-3.1b1-linux-intel-x86_64/easel/formats/fasta.odd.1
hmmer-3.1b1-linux-intel-x86_64/easel/formats/fasta.bad.1
hmmer-3.1b1-linux-intel-x86_64/easel/formats/uniprot
hmmer-3.1b1-linux-intel-x86_64/easel/formats/genbank.2
hmmer-3.1b1-linux-intel-x86_64/easel/formats/fasta
hmmer-3.1b1-linux-intel-x86_64/easel/formats/wag.dat
hmmer-3.1b1-linux-intel-x86_64/easel/formats/embl
hmmer-3.1b1-linux-intel-x86_64/easel/formats/fasta.bad.3
hmmer-3.1b1-linux-intel-x86_64/easel/formats/genbank
hmmer-3.1b1-linux-intel-x86_64/easel/formats/fasta.2
hmmer-3.1b1-linux-intel-x86_64/easel/formats/fasta.bad.2
hmmer-3.1b1-linux-intel-x86_64/easel/formats/BLOSUM62
hmmer-3.1b1-linux-intel-x86_64/easel/esl_weibull.h
hmmer-3.1b1-linux-intel-x86_64/easel/esl_ratematrix.c
hmmer-3.1b1-linux-intel-x86_64/libdivsufsort/
hmmer-3.1b1-linux-intel-x86_64/libdivsufsort/divsufsort.c
hmmer-3.1b1-linux-intel-x86_64/libdivsufsort/divsufsort.h.in
hmmer-3.1b1-linux-intel-x86_64/libdivsufsort/COPYING
hmmer-3.1b1-linux-intel-x86_64/libdivsufsort/VERSION
hmmer-3.1b1-linux-intel-x86_64/libdivsufsort/README
hmmer-3.1b1-linux-intel-x86_64/libdivsufsort/Makefile.in
hmmer-3.1b1-linux-intel-x86_64/libdivsufsort/AUTHORS
hmmer-3.1b1-linux-intel-x86_64/config.guess
hmmer-3.1b1-linux-intel-x86_64/COPYRIGHT
hmmer-3.1b1-linux-intel-x86_64/tutorial/
hmmer-3.1b1-linux-intel-x86_64/tutorial/Pkinase.sto
hmmer-3.1b1-linux-intel-x86_64/tutorial/minifam.h3f
hmmer-3.1b1-linux-intel-x86_64/tutorial/MADE1.sto
hmmer-3.1b1-linux-intel-x86_64/tutorial/7LESS_DROME
hmmer-3.1b1-linux-intel-x86_64/tutorial/fn3.sto
hmmer-3.1b1-linux-intel-x86_64/tutorial/globins45.fa
hmmer-3.1b1-linux-intel-x86_64/tutorial/HBB_HUMAN
hmmer-3.1b1-linux-intel-x86_64/tutorial/MADE1.hmm.h3i
hmmer-3.1b1-linux-intel-x86_64/tutorial/MADE1.hmm.h3p
hmmer-3.1b1-linux-intel-x86_64/tutorial/minifam
hmmer-3.1b1-linux-intel-x86_64/tutorial/Pkinase.hmm
hmmer-3.1b1-linux-intel-x86_64/tutorial/fn3.hmm
hmmer-3.1b1-linux-intel-x86_64/tutorial/globins4.out
hmmer-3.1b1-linux-intel-x86_64/tutorial/MADE1.hmm
hmmer-3.1b1-linux-intel-x86_64/tutorial/minifam.h3p
hmmer-3.1b1-linux-intel-x86_64/tutorial/globins4.sto
hmmer-3.1b1-linux-intel-x86_64/tutorial/MADE1.hmm.h3f
hmmer-3.1b1-linux-intel-x86_64/tutorial/minifam.h3i
hmmer-3.1b1-linux-intel-x86_64/tutorial/fn3.out
hmmer-3.1b1-linux-intel-x86_64/tutorial/MADE1.out
hmmer-3.1b1-linux-intel-x86_64/tutorial/minifam.h3m
hmmer-3.1b1-linux-intel-x86_64/tutorial/MADE1.hmm.h3m
hmmer-3.1b1-linux-intel-x86_64/tutorial/dna_target.fa
hmmer-3.1b1-linux-intel-x86_64/tutorial/globins4.hmm

In [6]:
cp hmmer-3.1b1-linux-intel-x86_64/binaries/hmmsearch ./bin

Install mothur


In [7]:
!wget http://www.mothur.org/w/images/8/88/Mothur.cen_64.zip -O mothur.zip


--2015-10-25 07:41:27--  http://www.mothur.org/w/images/8/88/Mothur.cen_64.zip
Resolving www.mothur.org (www.mothur.org)... 141.214.31.125
Connecting to www.mothur.org (www.mothur.org)|141.214.31.125|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 44310761 (42M) [application/zip]
Saving to: `mothur.zip'

100%[======================================>] 44,310,761  1.32M/s   in 32s     

2015-10-25 07:41:59 (1.33 MB/s) - `mothur.zip' saved [44310761/44310761]


In [8]:
!unzip mothur.zip


Archive:  mothur.zip
   creating: mothur/
  inflating: mothur/.DS_Store        
   creating: __MACOSX/
   creating: __MACOSX/mothur/
  inflating: __MACOSX/mothur/._.DS_Store  
   creating: mothur/blast/
  inflating: mothur/blast/.DS_Store  
   creating: __MACOSX/mothur/blast/
  inflating: __MACOSX/mothur/blast/._.DS_Store  
   creating: mothur/blast/bin/
  inflating: mothur/blast/bin/bl2seq  
   creating: __MACOSX/mothur/blast/bin/
  inflating: __MACOSX/mothur/blast/bin/._bl2seq  
  inflating: mothur/blast/bin/blastall  
  inflating: __MACOSX/mothur/blast/bin/._blastall  
  inflating: mothur/blast/bin/blastclust  
  inflating: __MACOSX/mothur/blast/bin/._blastclust  
  inflating: mothur/blast/bin/blastpgp  
  inflating: __MACOSX/mothur/blast/bin/._blastpgp  
  inflating: mothur/blast/bin/copymat  
  inflating: __MACOSX/mothur/blast/bin/._copymat  
  inflating: mothur/blast/bin/fastacmd  
  inflating: __MACOSX/mothur/blast/bin/._fastacmd  
  inflating: mothur/blast/bin/formatdb  
  inflating: __MACOSX/mothur/blast/bin/._formatdb  
  inflating: mothur/blast/bin/formatrpsdb  
  inflating: __MACOSX/mothur/blast/bin/._formatrpsdb  
  inflating: mothur/blast/bin/impala  
  inflating: __MACOSX/mothur/blast/bin/._impala  
  inflating: mothur/blast/bin/makemat  
  inflating: __MACOSX/mothur/blast/bin/._makemat  
  inflating: mothur/blast/bin/megablast  
  inflating: __MACOSX/mothur/blast/bin/._megablast  
  inflating: mothur/blast/bin/rpsblast  
  inflating: __MACOSX/mothur/blast/bin/._rpsblast  
  inflating: mothur/blast/bin/seedtop  
  inflating: __MACOSX/mothur/blast/bin/._seedtop  
  inflating: __MACOSX/mothur/blast/._bin  
  inflating: __MACOSX/mothur/._blast  
  inflating: mothur/CatchAllCmdL.exe  
  inflating: __MACOSX/mothur/._CatchAllCmdL.exe  
  inflating: mothur/mothur           
  inflating: mothur/uchime           

In [10]:
cp mothur/mothur ./bin

Install RDP mcclust tool


In [16]:
!wget http://athyra.oxli.org/~gjr/public2/misc/Clustering.tar.gz


--2015-10-25 07:49:35--  http://athyra.oxli.org/~gjr/public2/misc/Clustering.tar.gz
Resolving athyra.oxli.org (athyra.oxli.org)... 35.8.120.27
Connecting to athyra.oxli.org (athyra.oxli.org)|35.8.120.27|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 28617228 (27M) [application/x-gzip]
Saving to: `Clustering.tar.gz'

100%[======================================>] 28,617,228  2.43M/s   in 11s     

2015-10-25 07:49:47 (2.40 MB/s) - `Clustering.tar.gz' saved [28617228/28617228]


In [17]:
!tar -xzvf Clustering.tar.gz


Clustering/
Clustering/hadoop/
Clustering/hadoop/hadoop-0.18.3-core.jar
Clustering/nbproject/
Clustering/nbproject/project.properties
Clustering/nbproject/project.xml
Clustering/nbproject/genfiles.properties
Clustering/nbproject/build-impl.xml
Clustering/nbproject/configs/
Clustering/nbproject/configs/MCUPGMA.properties
Clustering/nbproject/configs/Pairwise.properties
Clustering/nbproject/configs/Create_Matrix.properties
Clustering/nbproject/configs/Main.properties
Clustering/nbproject/configs/TestCluster.properties
Clustering/nbproject/configs/GridwareTest.properties
Clustering/lib/
Clustering/lib/junit-4.8.2.jar
Clustering/lib/jaxb-impl-2.2.7.jar
Clustering/lib/commons-codec-1.8-sources.jar
Clustering/lib/jaxb-impl-2.2.7-sources.jar
Clustering/lib/jaxb-api-2.2.7.jar
Clustering/lib/junit-4.8.2-sources.jar
Clustering/lib/jsr173_api-1.0.jar
Clustering/lib/commons-cli-1.2-sources.jar
Clustering/lib/jaxb-core-2.2.7.jar
Clustering/lib/commons-io-2.4-sources.jar
Clustering/lib/istack-commons-runtime-2.16.jar
Clustering/lib/commons-cli-1.2-javadoc.jar
Clustering/lib/FastInfoset-1.2.12.jar
Clustering/lib/commons-codec-1.8.jar
Clustering/lib/junit-4.8.2-javadoc.jar
Clustering/lib/commons-cli-1.2.jar
Clustering/lib/commons-io-2.4.jar
Clustering/lib/commons-io-2.4-javadoc.jar
Clustering/lib/jaxb-impl-2.2.7-javadoc.jar
Clustering/lib/commons-codec-1.8-javadoc.jar
Clustering/.gitignore
Clustering/ivy.xml
Clustering/dist/
Clustering/dist/Clustering.jar
Clustering/dist/lib/
Clustering/dist/lib/ReadSeq.jar
Clustering/dist/lib/TaxonomyTree.jar
Clustering/dist/lib/SeqFilters.jar
Clustering/dist/lib/jaxb-api-2.2.7.jar
Clustering/dist/lib/jsr173_api-1.0.jar
Clustering/dist/lib/commons-codec-1.8.jar
Clustering/dist/lib/commons-cli-1.2.jar
Clustering/dist/lib/commons-io-2.4.jar
Clustering/dist/lib/jaxb-core-2.2.7.jar
Clustering/dist/lib/hadoop-0.18.3-core.jar
Clustering/dist/lib/AlignmentTools.jar
Clustering/dist/lib/jaxb-impl-2.2.7.jar
Clustering/dist/lib/junit-4.8.2.jar
Clustering/src/
Clustering/src/org/
Clustering/src/org/apache/
Clustering/src/org/apache/hadoop/
Clustering/src/org/apache/hadoop/mapred/
Clustering/src/org/apache/hadoop/mapred/ResortPartialResub.java
Clustering/src/org/apache/hadoop/mapred/ReadPartialResultFile.java
Clustering/src/org/apache/hadoop/mapred/CombinedIntermediateSortedReader.java
Clustering/src/org/apache/hadoop/mapred/ResortPartialResult.java
Clustering/src/org/apache/hadoop/mapred/SummarizeAttempts.java
Clustering/src/org/apache/hadoop/mapred/SortPartialResults.java
Clustering/src/edu/
Clustering/src/edu/msu/
Clustering/src/edu/msu/cme/
Clustering/src/edu/msu/cme/rdp/
Clustering/src/edu/msu/cme/rdp/taxatree/
Clustering/src/edu/msu/cme/rdp/taxatree/TreeBuilder.java
Clustering/src/edu/msu/cme/rdp/hadoop/
Clustering/src/edu/msu/cme/rdp/hadoop/distance/
Clustering/src/edu/msu/cme/rdp/hadoop/distance/mapred/
Clustering/src/edu/msu/cme/rdp/hadoop/distance/mapred/ByteSeqInputFormat.java
Clustering/src/edu/msu/cme/rdp/hadoop/distance/mapred/DistancePartitioner.java
Clustering/src/edu/msu/cme/rdp/hadoop/distance/mapred/DistanceReducer.java
Clustering/src/edu/msu/cme/rdp/hadoop/distance/mapred/keys/
Clustering/src/edu/msu/cme/rdp/hadoop/distance/mapred/keys/MatrixRange.java
Clustering/src/edu/msu/cme/rdp/hadoop/distance/mapred/keys/Comparison.java
Clustering/src/edu/msu/cme/rdp/hadoop/distance/mapred/keys/IntDistance.java
Clustering/src/edu/msu/cme/rdp/hadoop/distance/mapred/keys/DistanceAndComparison.java
Clustering/src/edu/msu/cme/rdp/hadoop/distance/mapred/DistanceAndComparisonMapper.java
Clustering/src/edu/msu/cme/rdp/hadoop/distance/sampler/
Clustering/src/edu/msu/cme/rdp/hadoop/distance/sampler/SamplerMain.java
Clustering/src/edu/msu/cme/rdp/hadoop/distance/sampler/SamplerInputFormat.java
Clustering/src/edu/msu/cme/rdp/hadoop/distance/sampler/SamplerReducer.java
Clustering/src/edu/msu/cme/rdp/hadoop/distance/DistancesMain.java
Clustering/src/edu/msu/cme/rdp/hadoop/oneoff/
Clustering/src/edu/msu/cme/rdp/hadoop/oneoff/DistancesMainOneOff.java
Clustering/src/edu/msu/cme/rdp/hadoop/oneoff/DistancePartitionerOneOff.java
Clustering/src/edu/msu/cme/rdp/hadoop/oneoff/HDFSEdgeReaderOneOff.java
Clustering/src/edu/msu/cme/rdp/hadoop/oneoff/ByteSeqInputFormatOneOff.java
Clustering/src/edu/msu/cme/rdp/hadoop/utils/
Clustering/src/edu/msu/cme/rdp/hadoop/utils/IntSeq.java
Clustering/src/edu/msu/cme/rdp/hadoop/utils/HDFSEdgeReader.java
Clustering/src/edu/msu/cme/rdp/hadoop/utils/HadoopClustering.java
Clustering/src/edu/msu/cme/rdp/hadoop/utils/AlignedIntSeqStore.java
Clustering/src/edu/msu/cme/rdp/hadoop/HadoopMain.java
Clustering/src/edu/msu/cme/pyro/
Clustering/src/edu/msu/cme/pyro/derep/
Clustering/src/edu/msu/cme/pyro/derep/SampleMapping.java
Clustering/src/edu/msu/cme/pyro/derep/Dereplicator.java
Clustering/src/edu/msu/cme/pyro/derep/RefreshMappings.java
Clustering/src/edu/msu/cme/pyro/derep/IdMapping.java
Clustering/src/edu/msu/cme/pyro/derep/ExplodeMappings.java
Clustering/src/edu/msu/cme/pyro/cluster/
Clustering/src/edu/msu/cme/pyro/cluster/Clustering.java
Clustering/src/edu/msu/cme/pyro/cluster/ClusterReplay.java
Clustering/src/edu/msu/cme/pyro/cluster/dist/
Clustering/src/edu/msu/cme/pyro/cluster/dist/MergeSortTest.java
Clustering/src/edu/msu/cme/pyro/cluster/dist/ThinEdge.java
Clustering/src/edu/msu/cme/pyro/cluster/dist/MergeDistsJob.java
Clustering/src/edu/msu/cme/pyro/cluster/dist/DistanceCalculator.java
Clustering/src/edu/msu/cme/pyro/cluster/dist/SlimDistMatrixSeq.java
Clustering/src/edu/msu/cme/pyro/cluster/dist/ThickEdge.java
Clustering/src/edu/msu/cme/pyro/cluster/dist/PairwiseDistance.java
Clustering/src/edu/msu/cme/pyro/cluster/upgma/
Clustering/src/edu/msu/cme/pyro/cluster/upgma/UPGMAClusterFactory.java
Clustering/src/edu/msu/cme/pyro/cluster/upgma/UPGMAState.java
Clustering/src/edu/msu/cme/pyro/cluster/upgma/CannotLoadMoreEdgesException.java
Clustering/src/edu/msu/cme/pyro/cluster/upgma/UPGMAReaderTest.java
Clustering/src/edu/msu/cme/pyro/cluster/upgma/EdgeComparator.java
Clustering/src/edu/msu/cme/pyro/cluster/upgma/ClusterMinEdge.java
Clustering/src/edu/msu/cme/pyro/cluster/upgma/BufferedRandomAccessFile.java
Clustering/src/edu/msu/cme/pyro/cluster/upgma/RandomAccessEdgeFile.java
Clustering/src/edu/msu/cme/pyro/cluster/upgma/UPGMAEdgeReader.java
Clustering/src/edu/msu/cme/pyro/cluster/upgma/UPGMAClusterEdges.java
Clustering/src/edu/msu/cme/pyro/cluster/upgma/Heap.java
Clustering/src/edu/msu/cme/pyro/cluster/ClusterMain.java
Clustering/src/edu/msu/cme/pyro/cluster/utils/
Clustering/src/edu/msu/cme/pyro/cluster/utils/RepresenativeSeqs.java
Clustering/src/edu/msu/cme/pyro/cluster/utils/Cluster.java
Clustering/src/edu/msu/cme/pyro/cluster/utils/CDHitToOTUTable.java
Clustering/src/edu/msu/cme/pyro/cluster/utils/ClusterFactory.java
Clustering/src/edu/msu/cme/pyro/cluster/utils/CDHitToRDP.java
Clustering/src/edu/msu/cme/pyro/cluster/utils/ClusterUtils.java
Clustering/src/edu/msu/cme/pyro/cluster/utils/ClusterEdges.java
Clustering/src/edu/msu/cme/pyro/cluster/utils/MergeSampleMapping.java
Clustering/src/edu/msu/cme/pyro/cluster/utils/AlignSeqMatch.java
Clustering/src/edu/msu/cme/pyro/cluster/utils/AbstractClusterFactory.java
Clustering/src/edu/msu/cme/pyro/cluster/io/
Clustering/src/edu/msu/cme/pyro/cluster/io/LocalEdgeReader.java
Clustering/src/edu/msu/cme/pyro/cluster/io/ClusterOutput.java
Clustering/src/edu/msu/cme/pyro/cluster/io/RFormatter.java
Clustering/src/edu/msu/cme/pyro/cluster/io/EdgeReader.java
Clustering/src/edu/msu/cme/pyro/cluster/io/ClusterToBiom.java
Clustering/src/edu/msu/cme/pyro/cluster/io/EdgeWriter.java
Clustering/src/edu/msu/cme/pyro/cluster/io/RDPClustParser.java
Clustering/src/edu/msu/cme/pyro/cluster/io/ClusterFileOutput.java
Clustering/build/
Clustering/build/empty/
Clustering/build/classes/
Clustering/build/classes/edu/
Clustering/build/classes/edu/msu/
Clustering/build/classes/edu/msu/cme/
Clustering/build/classes/edu/msu/cme/pyro/
Clustering/build/classes/edu/msu/cme/pyro/derep/
Clustering/build/classes/edu/msu/cme/pyro/derep/Dereplicator$DerepMode.class
Clustering/build/classes/edu/msu/cme/pyro/derep/Dereplicator.class
Clustering/build/classes/edu/msu/cme/pyro/derep/Dereplicator$DerepSeq.class
Clustering/build/classes/edu/msu/cme/pyro/derep/IdMapping.class
Clustering/build/classes/edu/msu/cme/pyro/derep/SampleMapping.class
Clustering/build/classes/edu/msu/cme/pyro/derep/RefreshMappings.class
Clustering/build/classes/edu/msu/cme/pyro/derep/ExplodeMappings.class
Clustering/build/classes/edu/msu/cme/pyro/cluster/
Clustering/build/classes/edu/msu/cme/pyro/cluster/Clustering$1.class
Clustering/build/classes/edu/msu/cme/pyro/cluster/dist/
Clustering/build/classes/edu/msu/cme/pyro/cluster/dist/ThinEdge.class
Clustering/build/classes/edu/msu/cme/pyro/cluster/dist/DistanceCalculator$PartialMatrixResult.class
Clustering/build/classes/edu/msu/cme/pyro/cluster/dist/MergeSortTest$1.class
Clustering/build/classes/edu/msu/cme/pyro/cluster/dist/DistanceCalculator$SequenceFile.class
Clustering/build/classes/edu/msu/cme/pyro/cluster/dist/MergeDistsJob.class
Clustering/build/classes/edu/msu/cme/pyro/cluster/dist/PairwiseDistance$SequenceFile.class
Clustering/build/classes/edu/msu/cme/pyro/cluster/dist/ThickEdge.class
Clustering/build/classes/edu/msu/cme/pyro/cluster/dist/DistanceCalculator$1.class
Clustering/build/classes/edu/msu/cme/pyro/cluster/dist/PairwiseDistance.class
Clustering/build/classes/edu/msu/cme/pyro/cluster/dist/MergeSortTest.class
Clustering/build/classes/edu/msu/cme/pyro/cluster/dist/DistanceCalculator.class
Clustering/build/classes/edu/msu/cme/pyro/cluster/dist/SlimDistMatrixSeq.class
Clustering/build/classes/edu/msu/cme/pyro/cluster/ClusterMain.class
Clustering/build/classes/edu/msu/cme/pyro/cluster/Clustering.class
Clustering/build/classes/edu/msu/cme/pyro/cluster/io/
Clustering/build/classes/edu/msu/cme/pyro/cluster/io/ClusterToBiom.class
Clustering/build/classes/edu/msu/cme/pyro/cluster/io/ClusterFileOutput.class
Clustering/build/classes/edu/msu/cme/pyro/cluster/io/RDPClustParser$Cutoff.class
Clustering/build/classes/edu/msu/cme/pyro/cluster/io/EdgeWriter.class
Clustering/build/classes/edu/msu/cme/pyro/cluster/io/ClusterOutput.class
Clustering/build/classes/edu/msu/cme/pyro/cluster/io/RFormatter.class
Clustering/build/classes/edu/msu/cme/pyro/cluster/io/RDPClustParser.class
Clustering/build/classes/edu/msu/cme/pyro/cluster/io/LocalEdgeReader.class
Clustering/build/classes/edu/msu/cme/pyro/cluster/io/EdgeReader.class
Clustering/build/classes/edu/msu/cme/pyro/cluster/io/RDPClustParser$ClusterSample.class
Clustering/build/classes/edu/msu/cme/pyro/cluster/upgma/
Clustering/build/classes/edu/msu/cme/pyro/cluster/upgma/UPGMAState$UPGMAStateHolder.class
Clustering/build/classes/edu/msu/cme/pyro/cluster/upgma/RandomAccessEdgeFile.class
Clustering/build/classes/edu/msu/cme/pyro/cluster/upgma/UPGMAEdgeReader.class
Clustering/build/classes/edu/msu/cme/pyro/cluster/upgma/UPGMAClusterFactory.class
Clustering/build/classes/edu/msu/cme/pyro/cluster/upgma/BufferedRandomAccessFile.class
Clustering/build/classes/edu/msu/cme/pyro/cluster/upgma/UPGMAState.class
Clustering/build/classes/edu/msu/cme/pyro/cluster/upgma/ClusterMinEdge.class
Clustering/build/classes/edu/msu/cme/pyro/cluster/upgma/EdgeComparator.class
Clustering/build/classes/edu/msu/cme/pyro/cluster/upgma/Heap.class
Clustering/build/classes/edu/msu/cme/pyro/cluster/upgma/UPGMAReaderTest.class
Clustering/build/classes/edu/msu/cme/pyro/cluster/upgma/CannotLoadMoreEdgesException.class
Clustering/build/classes/edu/msu/cme/pyro/cluster/upgma/UPGMAClusterEdges.class
Clustering/build/classes/edu/msu/cme/pyro/cluster/utils/
Clustering/build/classes/edu/msu/cme/pyro/cluster/utils/AbstractClusterFactory.class
Clustering/build/classes/edu/msu/cme/pyro/cluster/utils/CDHitToRDP$EasyClustFactory.class
Clustering/build/classes/edu/msu/cme/pyro/cluster/utils/ClusterFactory.class
Clustering/build/classes/edu/msu/cme/pyro/cluster/utils/Cluster.class
Clustering/build/classes/edu/msu/cme/pyro/cluster/utils/CDHitToRDP.class
Clustering/build/classes/edu/msu/cme/pyro/cluster/utils/ClusterUtils.class
Clustering/build/classes/edu/msu/cme/pyro/cluster/utils/AlignSeqMatch$AlignSeqMatchResult.class
Clustering/build/classes/edu/msu/cme/pyro/cluster/utils/AlignSeqMatch.class
Clustering/build/classes/edu/msu/cme/pyro/cluster/utils/MergeSampleMapping.class
Clustering/build/classes/edu/msu/cme/pyro/cluster/utils/ClusterUtils$ClusterParams.class
Clustering/build/classes/edu/msu/cme/pyro/cluster/utils/ClusterEdges.class
Clustering/build/classes/edu/msu/cme/pyro/cluster/utils/CDHitToOTUTable.class
Clustering/build/classes/edu/msu/cme/pyro/cluster/utils/CDHitToOTUTable$EasyClustFactory.class
Clustering/build/classes/edu/msu/cme/pyro/cluster/utils/RepresenativeSeqs.class
Clustering/build/classes/edu/msu/cme/pyro/cluster/ClusterReplay.class
Clustering/build/classes/edu/msu/cme/rdp/
Clustering/build/classes/edu/msu/cme/rdp/hadoop/
Clustering/build/classes/edu/msu/cme/rdp/hadoop/HadoopMain.class
Clustering/build/classes/edu/msu/cme/rdp/hadoop/utils/
Clustering/build/classes/edu/msu/cme/rdp/hadoop/utils/HDFSEdgeReader.class
Clustering/build/classes/edu/msu/cme/rdp/hadoop/utils/HadoopClustering.class
Clustering/build/classes/edu/msu/cme/rdp/hadoop/utils/HadoopClustering$1.class
Clustering/build/classes/edu/msu/cme/rdp/hadoop/utils/IntSeq.class
Clustering/build/classes/edu/msu/cme/rdp/hadoop/utils/AlignedIntSeqStore.class
Clustering/build/classes/edu/msu/cme/rdp/hadoop/distance/
Clustering/build/classes/edu/msu/cme/rdp/hadoop/distance/DistancesMain.class
Clustering/build/classes/edu/msu/cme/rdp/hadoop/distance/mapred/
Clustering/build/classes/edu/msu/cme/rdp/hadoop/distance/mapred/ByteSeqInputFormat$SeqInputSplit.class
Clustering/build/classes/edu/msu/cme/rdp/hadoop/distance/mapred/DistanceAndComparisonMapper.class
Clustering/build/classes/edu/msu/cme/rdp/hadoop/distance/mapred/ByteSeqInputFormat.class
Clustering/build/classes/edu/msu/cme/rdp/hadoop/distance/mapred/keys/
Clustering/build/classes/edu/msu/cme/rdp/hadoop/distance/mapred/keys/Comparison.class
Clustering/build/classes/edu/msu/cme/rdp/hadoop/distance/mapred/keys/DistanceAndComparison.class
Clustering/build/classes/edu/msu/cme/rdp/hadoop/distance/mapred/keys/IntDistance.class
Clustering/build/classes/edu/msu/cme/rdp/hadoop/distance/mapred/keys/MatrixRange.class
Clustering/build/classes/edu/msu/cme/rdp/hadoop/distance/mapred/keys/DistanceAndComparison$GroupingComparator.class
Clustering/build/classes/edu/msu/cme/rdp/hadoop/distance/mapred/DistancePartitioner.class
Clustering/build/classes/edu/msu/cme/rdp/hadoop/distance/mapred/DistanceReducer.class
Clustering/build/classes/edu/msu/cme/rdp/hadoop/distance/mapred/ByteSeqInputFormat$SeqRecordReader.class
Clustering/build/classes/edu/msu/cme/rdp/hadoop/distance/sampler/
Clustering/build/classes/edu/msu/cme/rdp/hadoop/distance/sampler/SamplerMain.class
Clustering/build/classes/edu/msu/cme/rdp/hadoop/distance/sampler/SamplerInputFormat.class
Clustering/build/classes/edu/msu/cme/rdp/hadoop/distance/sampler/SamplerReducer.class
Clustering/build/classes/edu/msu/cme/rdp/hadoop/oneoff/
Clustering/build/classes/edu/msu/cme/rdp/hadoop/oneoff/DistancesMainOneOff.class
Clustering/build/classes/edu/msu/cme/rdp/hadoop/oneoff/HDFSEdgeReaderOneOff.class
Clustering/build/classes/edu/msu/cme/rdp/hadoop/oneoff/ByteSeqInputFormatOneOff.class
Clustering/build/classes/edu/msu/cme/rdp/hadoop/oneoff/DistancePartitionerOneOff.class
Clustering/build/classes/edu/msu/cme/rdp/taxatree/
Clustering/build/classes/edu/msu/cme/rdp/taxatree/TreeBuilder$1.class
Clustering/build/classes/edu/msu/cme/rdp/taxatree/TreeBuilder.class
Clustering/build/classes/org/
Clustering/build/classes/org/apache/
Clustering/build/classes/org/apache/hadoop/
Clustering/build/classes/org/apache/hadoop/mapred/
Clustering/build/classes/org/apache/hadoop/mapred/CombinedIntermediateSortedReader.class
Clustering/build/classes/org/apache/hadoop/mapred/ResortPartialResub$ExpectedRange.class
Clustering/build/classes/org/apache/hadoop/mapred/SortPartialResults.class
Clustering/build/classes/org/apache/hadoop/mapred/CombinedIntermediateSortedReader$Holder.class
Clustering/build/classes/org/apache/hadoop/mapred/ReadPartialResultFile.class
Clustering/build/classes/org/apache/hadoop/mapred/ResortPartialResub.class
Clustering/build/classes/org/apache/hadoop/mapred/SummarizeAttempts.class
Clustering/build/classes/org/apache/hadoop/mapred/ResortPartialResult$ExpectedRange.class
Clustering/build/classes/org/apache/hadoop/mapred/ResortPartialResult.class
Clustering/build/built-jar.properties
Clustering/README.md
Clustering/mcupgma.py
Clustering/build.xml
Clustering/.git/
Clustering/.git/hooks/
Clustering/.git/hooks/update.sample
Clustering/.git/hooks/post-update.sample
Clustering/.git/hooks/pre-applypatch.sample
Clustering/.git/hooks/post-receive.sample
Clustering/.git/hooks/prepare-commit-msg.sample
Clustering/.git/hooks/pre-rebase.sample
Clustering/.git/hooks/post-commit.sample
Clustering/.git/hooks/commit-msg.sample
Clustering/.git/hooks/pre-commit.sample
Clustering/.git/hooks/applypatch-msg.sample
Clustering/.git/description
Clustering/.git/logs/
Clustering/.git/logs/refs/
Clustering/.git/logs/refs/heads/
Clustering/.git/logs/refs/heads/master
Clustering/.git/logs/HEAD
Clustering/.git/FETCH_HEAD
Clustering/.git/config
Clustering/.git/HEAD
Clustering/.git/branches/
Clustering/.git/index
Clustering/.git/refs/
Clustering/.git/refs/tags/
Clustering/.git/refs/remotes/
Clustering/.git/refs/remotes/origin/
Clustering/.git/refs/remotes/origin/HEAD
Clustering/.git/refs/heads/
Clustering/.git/refs/heads/master
Clustering/.git/packed-refs
Clustering/.git/info/
Clustering/.git/info/exclude
Clustering/.git/objects/
Clustering/.git/objects/info/
Clustering/.git/objects/pack/
Clustering/.git/objects/pack/pack-3daf23b0c75dd9ee353e2ec559db03c723f4097b.idx
Clustering/.git/objects/pack/pack-3daf23b0c75dd9ee353e2ec559db03c723f4097b.pack
Clustering/LICENSE
Clustering/manifest.mf

Install python packages

Comment out following cells if already have the packages installed


In [20]:
%%script bash
source ~/.bashrc

In [21]:
!pip install -U pip


You are using pip version 7.0.3, however version 7.1.2 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
Collecting pip
  Downloading pip-7.1.2-py2.py3-none-any.whl (1.1MB)
    100% |████████████████████████████████| 1.1MB 160kB/s 
Installing collected packages: pip
  Found existing installation: pip 7.0.3
    Uninstalling pip-7.0.3:
      Successfully uninstalled pip-7.0.3
Successfully installed pip-7.1.2

In [22]:
!pip install screed


Collecting screed
  Downloading screed-0.9.tar.gz (115kB)
    100% |████████████████████████████████| 118kB 708kB/s 
Collecting bz2file (from screed)
  Downloading bz2file-0.98.tar.gz
Installing collected packages: bz2file, screed
  Running setup.py install for bz2file
  Running setup.py install for screed
Successfully installed bz2file-0.98 screed-0.9

In [23]:
!pip install brewer2mpl


Collecting brewer2mpl
  Downloading brewer2mpl-1.4.1-py2.py3-none-any.whl
Installing collected packages: brewer2mpl
Successfully installed brewer2mpl-1.4.1

In [24]:
!pip install biom-format


Collecting biom-format
  Downloading biom-format-2.1.5.tar.gz (307kB)
    100% |████████████████████████████████| 311kB 474kB/s 
Collecting click (from biom-format)
  Downloading click-5.1-py2.py3-none-any.whl (65kB)
    100% |████████████████████████████████| 65kB 1.1MB/s 
Requirement already satisfied (use --upgrade to upgrade): numpy>=1.3.0 in /home/gjr/anaconda/lib/python2.7/site-packages (from biom-format)
Collecting future>=0.14.3 (from biom-format)
  Downloading future-0.15.2.tar.gz (1.6MB)
    100% |████████████████████████████████| 1.6MB 117kB/s 
Requirement already satisfied (use --upgrade to upgrade): scipy>=0.13.0 in /home/gjr/anaconda/lib/python2.7/site-packages (from biom-format)
Collecting pyqi (from biom-format)
  Downloading pyqi-0.3.2.tar.gz (240kB)
    100% |████████████████████████████████| 241kB 651kB/s 
Installing collected packages: click, future, pyqi, biom-format
  Running setup.py install for future
  Running setup.py install for pyqi
  Running setup.py install for biom-format
Successfully installed biom-format-2.1.5 click-5.1 future-0.15.2 pyqi-0.3.2

Install numpy, matplotlib, scipy, and pandas

Alternatively, you can install anaconda that have most popular python packages installed: https://store.continuum.io/cshop/anaconda/


In [25]:
# !pip install numpy matplotlib scipy pandas

check dependencies installed


In [31]:
import os
New_path = '{}:{}'.format('~/Desktop/SSUsearch/external_tools/bin/', os.environ['PATH'])
print New_path
os.environ.update({'PATH':New_path})


~/Desktop/SSUsearch/external_tools/bin/:~/Desktop/SSUsearch/external_tools/bin/:~/Desktop/SSUsearch/external_tools/bin/:/home/gjr/anaconda/bin:/usr/lib/lightdm/lightdm:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games

In [33]:
!make -f ~/Desktop/SSUsearch/Makefile tool_check Hmmsearch=hmmsearch Mothur=mothur Mcclust_jar=~/Desktop/SSUsearch/external_tools/Clustering/dist/Clustering.jar


*** Dependencies are installed

In [ ]: