deletions | additions       diff --git a/Qiime_test_results b/Qiime_test_results  new file mode 100644  index 0000000..776d5fd  --- /dev/null  +++ b/Qiime_test_results 
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[hannah@localhost qiime-deploy]$ source $HOME/.bashrc  [hannah@localhost qiime-deploy]$ print_qiime_config.py -t  System information  ==================  Platform: linux2  Python version: 2.7.3 (default, Jul 15 2013, 15:43:17) [GCC 4.7.2 20121109 (Red Hat 4.7.2-8)]  Python executable: /home/hannah/qiime_software/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_25  QIIME config values  ===================  blastmat_dir: /home/hannah/qiime_software/blast-2.2.22-release/data  sc_queue: all.q  topiaryexplorer_project_dir: None  pynast_template_alignment_fp: /home/hannah/qiime_software/core_set_aligned.fasta.imputed  cluster_jobs_fp: /home/hannah/qiime_software/qiime-1.7.0-release/bin/start_parallel_jobs.py  pynast_template_alignment_blastdb: None  assign_taxonomy_reference_seqs_fp: /home/hannah/qiime_software/gg_otus-12_10-release/rep_set/97_otus.fasta  torque_queue: friendlyq  template_alignment_lanemask_fp: /home/hannah/qiime_software/lanemask_in_1s_and_0s  jobs_to_start: 1  cloud_environment: False  qiime_scripts_dir: /home/hannah/qiime_software/qiime-1.7.0-release/bin  denoiser_min_per_core: 50  working_dir: /tmp/  python_exe_fp: /home/hannah/qiime_software/python-2.7.3-release/bin/python  temp_dir: /tmp/  blastall_fp: /home/hannah/qiime_software/blast-2.2.22-release/bin/blastall  seconds_to_sleep: 60  assign_taxonomy_id_to_taxonomy_fp: /home/hannah/qiime_software/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. ... FAIL  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 ... FAIL  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 ... FAIL  test_working_dir (__main__.Qiime_config)  working_dir, if set, is set to a valid path ... ok  ======================================================================  FAIL: test_ampliconnoise_install (__main__.Qiime_config)  AmpliconNoise install looks sane.  ----------------------------------------------------------------------  Traceback (most recent call last):  File "/home/hannah/qiime_software/qiime-1.7.0-release/bin/print_qiime_config.py", line 144, in test_ampliconnoise_install  "$PYRO_LOOKUP_FILE variable is not set. See %s for help." % url)  AssertionError: $PYRO_LOOKUP_FILE variable is not set. See http://qiime.org/install/install.html#ampliconnoise-install-notes for help.  ======================================================================  FAIL: test_denoiser_supported_version (__main__.Qiime_config)  denoiser aligner is ready to use  ----------------------------------------------------------------------  Traceback (most recent call last):  File "/home/hannah/qiime_software/qiime-1.7.0-release/bin/print_qiime_config.py", line 542, in test_denoiser_supported_version  "which components of QIIME you plan to use.")  AssertionError: Denoiser flowgram aligner not found or not executable.This may or may not be a problem depending on which components of QIIME you plan to use.  ======================================================================  FAIL: test_usearch_supported_version (__main__.Qiime_config)  usearch is in path and version is supported  ----------------------------------------------------------------------  Traceback (most recent call last):  File "/home/hannah/qiime_software/qiime-1.7.0-release/bin/print_qiime_config.py", line 678, in test_usearch_supported_version  "which components of QIIME you plan to use.")  AssertionError: usearch not found. This may or may not be a problem depending on which components of QIIME you plan to use.  ----------------------------------------------------------------------  Ran 35 tests in 0.915s  diff --git a/layout.md b/layout.md  index 7a9e325..16afb1a 100644  --- a/layout.md  +++ b/layout.md 
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Materials and Methods.tex  figures/zosteramarina1labels2/zosteramarina1labels2.png  Qiime_test_results  figures/sectioningschemelabels/figures/zosteramarina1labels1/figures/zosteramarina1labels/