Install QIIME (1.6.0)

Installation will be multiple versions type.

  • Install following this page GitHUb
apt-get install python-dev

mkdir /usr/share/qiime-1.6.0

cd /root/
rm -R qiime-deploy
rm -R qiime-deploy-conf
git clone git://github.com/qiime/qiime-deploy.git
git clone git://github.com/qiime/qiime-deploy-conf.git
cd qiime-deploy
python qiime-deploy.py /usr/share/qiime-1.6.0/ -f /root/qiime-deploy-conf/qiime-1.6.0/qiime.conf --force-remove-failed-dirs
  • Install usearch (=5.2.236)

Download from here http://www.drive5.com/usearch/download.html USEARCH

mkdir /usr/share/qiime-1.6.0/usearch-5.2.236-release/
cd /usr/share/qiime-1.6.0/usearch-5.2.236-release
wget /urltousearch/usearch
chmod +x usearch

Add path to activate script

export PATH=/usr/share/qiime-1.6.0/r-2.12.0-release/bin:/usr/share/qiime-1.6.0/cytoscape-2.7.0-release/.:/usr/share/qiime-1.6.0/qiime-1.6.0-release/bin:/usr/share/qiime-1.6.0/biom-format-1.1.1-release/bin:/usr/share/qiime-1.6.0/tax2tree-1.0-release/bin:/usr/share/qiime-1.6.0/pprospector-1.0.1-release/bin:/usr/share/qiime-1.6.0/pynast-1.2-release/bin:/usr/share/qiime-1.6.0/ipython-latest-repository-0985f236/bin:/usr/share/qiime-1.6.0/cython-0.17-release/bin:/usr/share/qiime-1.6.0/tornado-2.2.1-release/bin:/usr/share/qiime-1.6.0/pyzmq-2.1.9-release/bin:/usr/share/qiime-1.6.0/blast-2.2.22-release/bin:/usr/share/qiime-1.6.0/uclust-1.2.22-release/.:/usr/share/qiime-1.6.0/cdhit-3.1-release/.:/usr/share/qiime-1.6.0/rdpclassifier-2.2-release/.:/usr/share/qiime-1.6.0/muscle-3.8.31-release/.:/usr/share/qiime-1.6.0/parsinsert-1.0.4-release/.:/usr/share/qiime-1.6.0/pplacer-1.1-release/.:/usr/share/qiime-1.6.0/mothur-1.25.0-release/.:/usr/share/qiime-1.6.0/python-2.7.3-release/bin:/usr/share/qiime-1.6.0/bwa-0.6.2-release/.:/usr/share/qiime-1.6.0/fasttree-2.1.3-release/.:/usr/share/qiime-1.6.0/infernal-1.0.2-release/bin:/usr/share/qiime-1.6.0/vienna-1.8.4-release/.:/usr/share/qiime-1.6.0/chimeraslayer-4.29.2010-release/ChimeraSlayer:/usr/share/qiime-1.6.0/chimeraslayer-4.29.2010-release/NAST-iEr:/usr/share/qiime-1.6.0/drisee-1.2-release/.:/usr/share/qiime-1.6.0/ampliconnoise-1.27-release/Scripts:/usr/share/qiime-1.6.0/ampliconnoise-1.27-release/bin:/usr/share/qiime-1.6.0/raxml-7.3.0-release/.:/usr/share/qiime-1.6.0/rtax-0.983-release/.:/usr/share/qiime-1.6.0/cdbtools-10.11.2010-release/.:/usr/share/qiime-1.6.0/sourcetracker-0.9.4-release/.:/usr/share/qiime-1.6.0/blat-34-release/.:/usr/share/qiime-1.6.0/clearcut-1.0.9-release/.:/usr/share/qiime-1.6.0/usearch-5.2.236-release/.:$PATH
  • Install python-biopython
apt-get install python-biopython
  • Installation test
source /usr/share/qiime-1.6.0/activate.sh
print_qiime_config.py -t

System information
==================
         Platform:      linux2
   Python version:      2.7.3 (default, Jan 10 2013, 13:17:26)  [GCC 4.6.3]
Python executable:      /usr/share/qiime-1.6.0/python-2.7.3-release/bin/python

Dependency versions
===================
                     PyCogent version:  1.5.3
                        NumPy version:  1.5.1
                   matplotlib version:  1.1.0
                  biom-format version:  1.1.1
                QIIME library version:  1.6.0
                 QIIME script version:  1.6.0
        PyNAST version (if installed):  1.2
RDP Classifier version (if installed):  rdp_classifier-2.2.jar
          Java version (if installed):  1.6.0_24

QIIME config values
===================
                     blastmat_dir:      /usr/share/qiime-1.6.0/blast-2.2.22-release/data
                         sc_queue:      all.q
      topiaryexplorer_project_dir:      None
     pynast_template_alignment_fp:      /usr/share/qiime-1.6.0/core_set_aligned.fasta.imputed
                  cluster_jobs_fp:      /usr/share/qiime-1.6.0/qiime-1.6.0-release/bin/start_parallel_jobs.py
pynast_template_alignment_blastdb:      None
assign_taxonomy_reference_seqs_fp:      /usr/share/qiime-1.6.0/gg_otus-12_10-release/rep_set/97_otus.fasta
                     torque_queue:      friendlyq
              qiime_test_data_dir:      None
   template_alignment_lanemask_fp:      /usr/share/qiime-1.6.0/lanemask_in_1s_and_0s
                    jobs_to_start:      1
                cloud_environment:      False
                qiime_scripts_dir:      /usr/share/qiime-1.6.0/qiime-1.6.0-release/bin
            denoiser_min_per_core:      50
                      working_dir:      /tmp/
                    python_exe_fp:      /usr/share/qiime-1.6.0/python-2.7.3-release/bin/python
                         temp_dir:      /tmp/
                      blastall_fp:      /usr/share/qiime-1.6.0/blast-2.2.22-release/bin/blastall
                 seconds_to_sleep:      60
assign_taxonomy_id_to_taxonomy_fp:      /usr/share/qiime-1.6.0/gg_otus-12_10-release/taxonomy/97_otu_taxonomy.txt


running checks:

test_FastTree_supported_version (__main__.Qiime_config)
FastTree is in path and version is supported ... ok
test_INFERNAL_supported_version (__main__.Qiime_config)
INFERNAL is in path and version is supported ... ok
test_ParsInsert_supported_version (__main__.Qiime_config)
ParsInsert is in path and version is supported ... ok
test_R_supported_version (__main__.Qiime_config)
R is in path and version is supported ... ok
test_ampliconnoise_install (__main__.Qiime_config)
AmpliconNoise install looks sane. ... ok
test_blast_supported_version (__main__.Qiime_config)
blast is in path and version is supported ... ok
test_blastall_fp (__main__.Qiime_config)
blastall_fp is set to a valid path ... ok
test_blastmat_dir (__main__.Qiime_config)
blastmat_dir is set to a valid path. ... ok
test_cdbtools_supported_version (__main__.Qiime_config)
cdbtools is in path and version is supported ... ok
test_cdhit_supported_version (__main__.Qiime_config)
cd-hit is in path and version is supported ... ok
test_chimeraSlayer_install (__main__.Qiime_config)
no obvious problems with ChimeraSlayer install ... ok
test_clearcut_supported_version (__main__.Qiime_config)
clearcut is in path and version is supported ... ok
test_cluster_jobs_fp (__main__.Qiime_config)
cluster_jobs_fp is set to a valid path and is executable ... ok
test_denoiser_supported_version (__main__.Qiime_config)
denoiser aligner is ready to use ... ok
test_for_obsolete_values (__main__.Qiime_config)
local qiime_config has no extra params ... ok
test_gdata_install (__main__.Qiime_config)
gdata is installed ... ok
test_matplotlib_suported_version (__main__.Qiime_config)
maptplotlib version is supported ... ok
test_mothur_supported_version (__main__.Qiime_config)
mothur is in path and version is supported ... ok
test_muscle_supported_version (__main__.Qiime_config)
muscle is in path and version is supported ... ok
test_numpy_suported_version (__main__.Qiime_config)
numpy version is supported ... ok
test_pplacer_supported_version (__main__.Qiime_config)
pplacer is in path and version is supported ... ok
test_pynast_suported_version (__main__.Qiime_config)
pynast version is supported ... ok
test_pynast_template_alignment_blastdb_fp (__main__.Qiime_config)
pynast_template_alignment_blastdb, if set, is set to a valid path ... ok
test_pynast_template_alignment_fp (__main__.Qiime_config)
pynast_template_alignment, if set, is set to a valid path ... ok
test_python_exe_fp (__main__.Qiime_config)
python_exe_fp is set to a working python env ... ok
test_python_supported_version (__main__.Qiime_config)
python is in path and version is supported ... ok
test_qiime_scripts_dir (__main__.Qiime_config)
qiime_scripts_dir, if set, is set to a valid path ... ok
test_qiime_test_data_dir (__main__.Qiime_config)
qiime_test_data_dir, if set, is set to a valid path ... ok
test_raxmlHPC_supported_version (__main__.Qiime_config)
raxmlHPC is in path and version is supported ... ok
test_rtax_supported_version (__main__.Qiime_config)
rtax is in path and version is supported ... ok
test_temp_dir (__main__.Qiime_config)
temp_dir, if set, is set to a valid path ... ok
test_template_alignment_lanemask_fp (__main__.Qiime_config)
template_alignment_lanemask, if set, is set to a valid path ... ok
test_uclust_supported_version (__main__.Qiime_config)
uclust is in path and version is supported ... ok
test_usearch_supported_version (__main__.Qiime_config)
usearch is in path and version is supported ... ok
test_working_dir (__main__.Qiime_config)
working_dir, if set, is set to a valid path ... ok

----------------------------------------------------------------------
Ran 35 tests in 0.859s

OK
 
 
rachaelx/qiime160.txt ยท Last modified: 2013/06/06 16:02 by giancarlo

Developers: CNR Ceris IT Office and Library
Giancarlo Birello (g.birello _@_ ceris.cnr.it) and Anna Perin (a.perin _@_ ceris.cnr.it)
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