Fix Qiime installation test errors (1.5.0)

USEARCH

Copy usearch folder from Qiime virtual image installation

root@rachaelx:/usr/share/qiime_software# scp -r user@qiime_virtualbox:/usr/share/qiime_software/usearch-5.2.32-release ./

Then add path in activate.sh

root@rachaelx:/usr/share/qiime_software# nano -w activate.sh

root@rachaelx:/usr/share/qiime_software# cat activate.sh |grep search
export PATH=/usr/share/qiime_software/r-2.12.0-release/bin:/usr/share/qiime_software/qiime-1.5.0-release/bin:/usr/share/qiime_software/cytoscape-2.7.0-release/.:/usr/share/qiime_software/pprospector-1.0.1-release/bin:/usr/share/qiime_software/pynast-1.1-release/bin:/usr/share/qiime_software/biom-format-0.9.3-release/scripts/:/usr/share/qiime_software/ipython-0.13-release/bin:/usr/share/qiime_software/tornado-2.2.1-release/bin:/usr/share/qiime_software/blast-2.2.22-release/bin:/usr/share/qiime_software/pyzmq-2.1.9-release/bin:/usr/share/qiime_software/python-2.7.1-release/bin:/usr/share/qiime_software/uclust-1.2.22-release/.:/usr/share/qiime_software/cdhit-3.1-release/.:/usr/share/qiime_software/rdpclassifier-2.2-release/.:/usr/share/qiime_software/muscle-3.8.31-release/.:/usr/share/qiime_software/parsinsert-1.0.4-release/.:/usr/share/qiime_software/mothur-1.25.0-release/.:/usr/share/qiime_software/pplacer-1.1-release/.:/usr/share/qiime_software/fasttree-2.1.3-release/.:/usr/share/qiime_softw are/infernal-1.0.2-release/bin:/usr/share/qiime_software/vienna-1.8.4-release/.:/usr/share/qiime_software/chimeraslayer-4.29.2010-release/ChimeraSlayer:/usr/share/qiime_software/chimeraslayer-4.29.2010-release/NAST-iEr:/usr/share/qiime_software/drisee-1.2-release/.:/usr/share/qiime_software/cdbtools-10.11.2010-release/.:/usr/share/qiime_software/ampliconnoise-1.25-release/Scripts:/usr/share/qiime_software/ampliconnoise-1.25-release/bin:/usr/share/qiime_software/raxml-7.3.0-release/.:/usr/share/qiime_software/clearcut-1.0.9-release/.:/usr/share/qiime_software/rtax-0.982-release/.:/usr/share/qiime_software/usearch-5.2.32-release/.:$PATH

RTAX

Copy rtax 0.981 folder from Qiime virtual image installation

root@rachaelx:/usr/share/qiime_software# scp -r user@qiime_virtualbox:/usr/share/qiime_software/rtax-0.981-release ./

Then change path rtax-0.982-release to rtax-0.981-releas in activate.sh

root@rachaelx:/usr/share/qiime_software# nano -w activate.sh

root@rachaelx:/usr/share/qiime_software# cat activate.sh |grep rtax
export PATH=/usr/share/qiime_software/r-2.12.0-release/bin:/usr/share/qiime_software/qiime-1.5.0-release/bin:/usr/share/qiime_software/cytoscape-2.7.0-release/.:/usr/share/qiime_software/pprospector-1.0.1-release/bin:/usr/share/qiime_software/pynast-1.1-release/bin:/usr/share/qiime_software/biom-format-0.9.3-release/scripts/:/usr/share/qiime_software/ipython-0.13-release/bin:/usr/share/qiime_software/tornado-2.2.1-release/bin:/usr/share/qiime_software/blast-2.2.22-release/bin:/usr/share/qiime_software/pyzmq-2.1.9-release/bin:/usr/share/qiime_software/python-2.7.1-release/bin:/usr/share/qiime_software/uclust-1.2.22-release/.:/usr/share/qiime_software/cdhit-3.1-release/.:/usr/share/qiime_software/rdpclassifier-2.2-release/.:/usr/share/qiime_software/muscle-3.8.31-release/.:/usr/share/qiime_software/parsinsert-1.0.4-release/.:/usr/share/qiime_software/mothur-1.25.0-release/.:/usr/share/qiime_software/pplacer-1.1-release/.:/usr/share/qiime_software/fasttree-2.1.3-release/.:/usr/share/qiime_softw are/infernal-1.0.2-release/bin:/usr/share/qiime_software/vienna-1.8.4-release/.:/usr/share/qiime_software/chimeraslayer-4.29.2010-release/ChimeraSlayer:/usr/share/qiime_software/chimeraslayer-4.29.2010-release/NAST-iEr:/usr/share/qiime_software/drisee-1.2-release/.:/usr/share/qiime_software/cdbtools-10.11.2010-release/.:/usr/share/qiime_software/ampliconnoise-1.25-release/Scripts:/usr/share/qiime_software/ampliconnoise-1.25-release/bin:/usr/share/qiime_software/raxml-7.3.0-release/.:/usr/share/qiime_software/clearcut-1.0.9-release/.:/usr/share/qiime_software/rtax-0.981-release/.:/usr/share/qiime_software/usearch-5.2.32-release/.:$PATH

MOTHUR

Install missed package

root@rachaelx:~# apt-get install libreadline5

Replace mothur folder with the mothur folder on Qiime virtual image installation

root@rachaelx:/usr/share/qiime_software# mv mothur-1.25.0-release mothur-1.25.0-release.ORI
root@rachaelx:/usr/share/qiime_software# scp -r user@qiime_virtualbox:/usr/share/qiime_software/mothur-1.25.0-release ./

DENOISER

Compile missed bin and install it

root@rachaelx:~# cd /usr/share/qiime_software/qiime-1.5.0-release/qiime/support_files/denoiser/FlowgramAlignment
root@rachaelx:~# make
root@rachaelx:~# make install
root@rachaelx:~# mkdir /usr/share/qiime_software/qiime-1.5.0-release/lib/qiime/support_files/denoiser/bin
root@rachaelx:~# cp /usr/share/qiime_software/qiime-1.5.0-release/qiime/support_files/denoiser/bin/FlowgramAli_4frame /usr/share/qiime_software/qiime-1.5.0-release/lib/qiime/support_files/denoiser/bin/

PYTHON

Edit these files

/usr/share/qiime_software/qiime-1.5.0-release/bin/print_qiime_config.py
/usr/share/qiime_software/qiime-1.5.0-release/build/scripts-2.7/print_qiime_config.py
/usr/share/qiime_software/qiime-1.5.0-release/scripts/print_qiime_config.py

and change min_unacceptable_version from (2,7,2) to (2,7,3)

Qiime installation test without errors

user@rachaelx:~$ print_qiime_config.py -t

System information
==================
         Platform:    linux2
   Python version:    2.7.3 (default, Aug  1 2012, 05:25:23)  [GCC 4.6.3]
Python executable:    /usr/share/qiime_software/python-2.7.1-release/bin/python

Dependency versions
===================
                     PyCogent version:    1.5.1
                        NumPy version:    1.5.1
                   matplotlib version:    1.1.0
                  biom-format version:    0.9.3
                QIIME library version:    1.5.0
                 QIIME script version:    1.5.0
        PyNAST version (if installed):    1.1
RDP Classifier version (if installed):    rdp_classifier-2.2.jar

QIIME config values
===================
                     blastmat_dir:    /usr/share/qiime_software/blast-2.2.22-release/data
                         sc_queue:    all.q
      topiaryexplorer_project_dir:    None
     pynast_template_alignment_fp:    /usr/share/qiime_software/core_set_aligned.fasta.imputed
                  cluster_jobs_fp:    /usr/share/qiime_software/qiime-1.5.0-release/bin/start_parallel_jobs.py
pynast_template_alignment_blastdb:    None
assign_taxonomy_reference_seqs_fp:    /usr/share/qiime_software/gg_otus-4feb2011-release/rep_set/gg_97_otus_4feb2011.fasta
                     torque_queue:    friendlyq
              qiime_test_data_dir:    None
   template_alignment_lanemask_fp:    /usr/share/qiime_software/lanemask_in_1s_and_0s
                    jobs_to_start:    1
                cloud_environment:    False
                qiime_scripts_dir:    /usr/share/qiime_software/qiime-1.5.0-release/bin
            denoiser_min_per_core:    50
                      working_dir:    /tmp/
                    python_exe_fp:    /usr/share/qiime_software/python-2.7.1-release/bin/python
                         temp_dir:    /tmp/
                      blastall_fp:    /usr/share/qiime_software/blast-2.2.22-release/bin/blastall
                 seconds_to_sleep:    60
assign_taxonomy_id_to_taxonomy_fp:    /usr/share/qiime_software/gg_otus-4feb2011-release/taxonomies/greengenes_tax_rdp_train.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_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 34 tests in 0.675s

OK