====== Install QIIME (1.7.0) ======
Installation will be multiple versions type.
* Install following this page [[https://github.com/qiime/qiime-deploy|GitHUb]]
mkdir /usr/share/qiime-1.7.0
cd /root/
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-1.7.0/ -f /root/qiime-deploy-conf/qiime-1.7.0/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-1.7.0/usearch-5.2.236-release/
cd /usr/share/qiime-1.7.0/usearch-5.2.236-release
wget /urltousearch/usearch
chmod +x usearch
Add path to activate script
export PATH=.............:/usr/share/qiime-1.7.0/usearch-5.2.236-release/.:$PATH
* Install pplacer (=1.1)
Download from here [[http://matsen.fhcrc.org/pplacer/|pplacer]]
wget http://matsen.fhcrc.org/pplacer/builds/pplacer-v1.1-Linux.tar.gz
tar -xvzf pplacer-v1.1-Linux.tar.gz
mv pplacer-v1.1.alpha14-Linux-3.2.0 /usr/share/qiime-1.7.0/
Add path to activate script
export PATH=.............:/usr/share/qiime-1.7.0/pplacer-v1.1.alpha14-Linux-3.2.0/.:/usr/share/qiime-1.7.0/pplacer-v1.1.alpha14-Linux-3.2.0/scripts/.:$PATH
* Installation test
source /usr/share/qiime-1.7.0/activate.sh
print_qiime_config.py -t
System information
==================
Platform: linux2
Python version: 2.7.3 (default, Jun 6 2013, 13:11:23) [GCC 4.6.3]
Python executable: /usr/share/qiime-1.7.0/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: 1.1.2
QIIME library version: 1.7.0
QIIME script version: 1.7.0
PyNAST version (if installed): 1.2
RDP Classifier version (if installed): rdp_classifier-2.2.jar
Java version (if installed): 1.7.0_21
QIIME config values
===================
blastmat_dir: /usr/share/qiime-1.7.0/blast-2.2.22-release/data
sc_queue: all.q
topiaryexplorer_project_dir: None
pynast_template_alignment_fp: /usr/share/qiime-1.7.0/core_set_aligned.fasta.imputed
cluster_jobs_fp: /usr/share/qiime-1.7.0/qiime-1.7.0-release/bin/start_parallel_jobs.py
pynast_template_alignment_blastdb: None
assign_taxonomy_reference_seqs_fp: /usr/share/qiime-1.7.0/gg_otus-12_10-release/rep_set/97_otus.fasta
torque_queue: friendlyq
template_alignment_lanemask_fp: /usr/share/qiime-1.7.0/lanemask_in_1s_and_0s
jobs_to_start: 1
cloud_environment: False
qiime_scripts_dir: /usr/share/qiime-1.7.0/qiime-1.7.0-release/bin
denoiser_min_per_core: 50
working_dir: /tmp/
python_exe_fp: /usr/share/qiime-1.7.0/python-2.7.3-release/bin/python
temp_dir: /tmp/
blastall_fp: /usr/share/qiime-1.7.0/blast-2.2.22-release/bin/blastall
seconds_to_sleep: 60
assign_taxonomy_id_to_taxonomy_fp: /usr/share/qiime-1.7.0/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_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_sourcetracker_installed (__main__.Qiime_config)
sourcetracker is installed ... 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 0.763s
OK