This pipeline requires:
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.
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
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/
hmmer-3.1b1-linux-intel-x86_64/testsuite/i17-stdin.pl
hmmer-3.1b1-linux-intel-x86_64/testsuite/ecori.fa
hmmer-3.1b1-linux-intel-x86_64/testsuite/i15-hmmconvert.pl
hmmer-3.1b1-linux-intel-x86_64/testsuite/i6-hmmalign-mapali.pl
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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
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
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
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
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
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 [ ]:
Content source: dib-lab/SSUsearch
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