In [13]:
ir="/usr/local/bin/irods3.2.icmds.mac.intel/"
In [15]:
!{ir}/icd /iplant/home/che625/Larvae_trimmed
In [16]:
!{ir}/ipwd
/iplant/home/che625/Larvae_trimmed

In [17]:
!ils
/iplant/home/che625/Larvae_trimmed:
  mcf_M1_R1.fastq
  mcf_M1_R2.fastq
  mcf_M3_R1.fastq
  mcf_M3_R2.fastq
  mcf_T1D3_R1.fastq
  mcf_T1D3_R2.fastq
  mcf_T1D5_R1.fastq
  mcf_T1D5_R2.fastq
  mcf_T3D3_R1.fastq
  mcf_T3D3_R2.fastq
  mcf_T3D5_R1.fastq
  mcf_T3D5_R2.fastq
  C- /iplant/home/che625/Larvae_trimmed/BSMAP
  C- /iplant/home/che625/Larvae_trimmed/FastQC

In [18]:
!icd /iplant/home/che625/Larvae_trimmed/BSMAP
In [19]:
!ils
/iplant/home/che625/Larvae_trimmed/BSMAP:
  C- /iplant/home/che625/Larvae_trimmed/BSMAP/BSMAP_analysis_M1-2014-04-02-17-01-52.200
  C- /iplant/home/che625/Larvae_trimmed/BSMAP/BSMAP_analysis_M3-2014-04-02-17-07-53.798
  C- /iplant/home/che625/Larvae_trimmed/BSMAP/BSMAP_analysis_T1D3-2014-04-02-17-10-34.071
  C- /iplant/home/che625/Larvae_trimmed/BSMAP/BSMAP_analysis_T1D5-2014-04-02-17-13-04.225
  C- /iplant/home/che625/Larvae_trimmed/BSMAP/BSMAP_analysis_T3D3-2014-04-02-17-14-56.555

In [23]:
!icd /iplant/home/che625/Larvae_trimmed/BSMAP/BSMAP_analysis_M1-2014-04-02-17-01-52.200/logs
In [24]:
!ils
/iplant/home/che625/Larvae_trimmed/BSMAP/BSMAP_analysis_M1-2014-04-02-17-01-52.200/logs:
  condor-0-input-0-stderr
  condor-0-input-0-stdout
  condor-0-input-1-stderr
  condor-0-input-1-stdout
  condor-0-input-2-stderr
  condor-0-input-2-stdout
  condor-stderr-0
  condor-stdout-0
  iplant.cmd
  iplant.sh
  output-last-stderr
  output-last-stdout
  script-condor-log
  script-error.log
  script-output.log

In [25]:
!iget /iplant/home/che625/Larvae_trimmed/BSMAP/BSMAP_analysis_M1-2014-04-02-17-01-52.200/logs/condor-stdout-0 /Volumes/web/Mollusk/bs_larvae_exp/AdaptorTrimmed_BSMAP_files/M1
In [26]:
!icd /iplant/home/che625/Larvae_trimmed/BSMAP/BSMAP_analysis_M3-2014-04-02-17-07-53.798/logs
In [27]:
!ils
/iplant/home/che625/Larvae_trimmed/BSMAP/BSMAP_analysis_M3-2014-04-02-17-07-53.798/logs:
  condor-0-input-0-stderr
  condor-0-input-0-stdout
  condor-0-input-1-stderr
  condor-0-input-1-stdout
  condor-0-input-2-stderr
  condor-0-input-2-stdout
  condor-stderr-0
  condor-stdout-0
  iplant.cmd
  iplant.sh
  output-last-stderr
  output-last-stdout
  script-condor-log
  script-error.log
  script-output.log

In [28]:
!iget /iplant/home/che625/Larvae_trimmed/BSMAP/BSMAP_analysis_M3-2014-04-02-17-07-53.798/logs/condor-stdout-0 /Volumes/web/Mollusk/bs_larvae_exp/AdaptorTrimmed_BSMAP_files/M3
In [31]:
!icd /iplant/home/che625/Larvae_trimmed/BSMAP/BSMAP_analysis_T1D3-2014-04-02-17-10-34.071/logs
In [32]:
!ils
/iplant/home/che625/Larvae_trimmed/BSMAP/BSMAP_analysis_T1D3-2014-04-02-17-10-34.071/logs:
  condor-0-input-0-stderr
  condor-0-input-0-stdout
  condor-0-input-1-stderr
  condor-0-input-1-stdout
  condor-0-input-2-stderr
  condor-0-input-2-stdout
  condor-stderr-0
  condor-stdout-0
  iplant.cmd
  iplant.sh
  output-last-stderr
  output-last-stdout
  script-condor-log
  script-error.log
  script-output.log

In [33]:
!iget /iplant/home/che625/Larvae_trimmed/BSMAP/BSMAP_analysis_T1D3-2014-04-02-17-10-34.071/logs/condor-stdout-0 /Volumes/web/Mollusk/bs_larvae_exp/AdaptorTrimmed_BSMAP_files/T1D3
In [34]:
!icd /iplant/home/che625/Larvae_trimmed/BSMAP/BSMAP_analysis_T1D5-2014-04-02-17-13-04.225/logs
In [35]:
!ils
/iplant/home/che625/Larvae_trimmed/BSMAP/BSMAP_analysis_T1D5-2014-04-02-17-13-04.225/logs:
  condor-0-input-0-stderr
  condor-0-input-0-stdout
  condor-0-input-1-stderr
  condor-0-input-1-stdout
  condor-0-input-2-stderr
  condor-0-input-2-stdout
  condor-stderr-0
  condor-stdout-0
  iplant.cmd
  iplant.sh
  output-last-stderr
  output-last-stdout
  script-condor-log
  script-error.log
  script-output.log

In [36]:
!iget /iplant/home/che625/Larvae_trimmed/BSMAP/BSMAP_analysis_T1D5-2014-04-02-17-13-04.225/logs/condor-stdout-0 /Volumes/web/Mollusk/bs_larvae_exp/AdaptorTrimmed_BSMAP_files/T1D5
In [37]:
!icd /iplant/home/che625/Larvae_trimmed/BSMAP/BSMAP_analysis_T3D3-2014-04-02-17-14-56.555/logs
In [38]:
!ils
/iplant/home/che625/Larvae_trimmed/BSMAP/BSMAP_analysis_T3D3-2014-04-02-17-14-56.555/logs:
  condor-0-input-0-stderr
  condor-0-input-0-stdout
  condor-0-input-1-stderr
  condor-0-input-1-stdout
  condor-0-input-2-stderr
  condor-0-input-2-stdout
  condor-stderr-0
  condor-stdout-0
  iplant.cmd
  iplant.sh
  output-last-stderr
  output-last-stdout
  script-condor-log
  script-error.log
  script-output.log

In [40]:
!iget /iplant/home/che625/Larvae_trimmed/BSMAP/BSMAP_analysis_T3D3-2014-04-02-17-14-56.555/logs/condor-stdout-0 /Volumes/web/Mollusk/bs_larvae_exp/AdaptorTrimmed_BSMAP_files/T3D3
In [46]:
!icd /iplant/home/che625/Larvae_trimmed/BSMAP
In [47]:
!ils
/iplant/home/che625/Larvae_trimmed/BSMAP:
  C- /iplant/home/che625/Larvae_trimmed/BSMAP/BSMAP_analysis_M1-2014-04-02-17-01-52.200
  C- /iplant/home/che625/Larvae_trimmed/BSMAP/BSMAP_analysis_M3-2014-04-02-17-07-53.798
  C- /iplant/home/che625/Larvae_trimmed/BSMAP/BSMAP_analysis_T1D3-2014-04-02-17-10-34.071
  C- /iplant/home/che625/Larvae_trimmed/BSMAP/BSMAP_analysis_T1D5-2014-04-02-17-13-04.225
  C- /iplant/home/che625/Larvae_trimmed/BSMAP/BSMAP_analysis_T3D3-2014-04-02-17-14-56.555
  C- /iplant/home/che625/Larvae_trimmed/BSMAP/BSMAP_analysis_T3D5-2014-04-03-11-33-15.038

In [48]:
!icd /iplant/home/che625/Larvae_trimmed/BSMAP/BSMAP_analysis_T3D5-2014-04-03-11-33-15.038/logs
In [49]:
!ils
/iplant/home/che625/Larvae_trimmed/BSMAP/BSMAP_analysis_T3D5-2014-04-03-11-33-15.038/logs:
  condor-0-input-0-stderr
  condor-0-input-0-stdout
  condor-0-input-1-stderr
  condor-0-input-1-stdout
  condor-0-input-2-stderr
  condor-0-input-2-stdout
  condor-stderr-0
  condor-stdout-0
  iplant.cmd
  iplant.sh
  output-last-stderr
  output-last-stdout
  script-condor-log
  script-error.log
  script-output.log

In [50]:
!iget /iplant/home/che625/Larvae_trimmed/BSMAP/BSMAP_analysis_T3D5-2014-04-03-11-33-15.038/logs/condor-stdout-0 /Volumes/web/Mollusk/bs_larvae_exp/AdaptorTrimmed_BSMAP_files/T3D5
In [18]:
#NOTEBOOK NAME
nb='Download_BSMAP_Larvae_adaptortrimmed'

#NOTEBOOK LOCATION
nbloc='/Users/claireolson/Dropbox/Lab\ \(1\)/IPython_nbs/Claire/'



#TIMESTAMP
date=!date +%m%d_%H%M
#LOCATION OF POST DIRECTORY
post='/Volumes/web/Mollusk/ipython_entries/'
In [19]:
cd {post}
/Volumes/web/Mollusk/ipython_entries

In [20]:
!ipython nbconvert {nbloc}{nb} --to html --template full --output {nb}{date}
[NbConvertApp] Using existing profile dir: u'/Users/claireolson/.ipython/profile_default'
[NbConvertApp] WARNING | pattern u'/Users/claireolson/Dropbox/Lab (1)/IPython_nbs/Claire/Download_BSMAP_Larvae_adaptortrimmed' matched no files
This application is used to convert notebook files (*.ipynb) to various other
formats.

WARNING: THE COMMANDLINE INTERFACE MAY CHANGE IN FUTURE RELEASES.

Options
-------

Arguments that take values are actually convenience aliases to full
Configurables, whose aliases are listed on the help line. For more information
on full configurables, see '--help-all'.

--debug
    set log level to logging.DEBUG (maximize logging output)
--init
    Initialize profile with default config files.  This is equivalent
    to running `ipython profile create <profile>` prior to startup.
--quiet
    set log level to logging.CRITICAL (minimize logging output)
--stdout
    Write notebook output to stdout instead of files.
--profile=<Unicode> (BaseIPythonApplication.profile)
    Default: u'default'
    The IPython profile to use.
--ipython-dir=<Unicode> (BaseIPythonApplication.ipython_dir)
    Default: u'/Users/claireolson/.ipython'
    The name of the IPython directory. This directory is used for logging
    configuration (through profiles), history storage, etc. The default is
    usually $HOME/.ipython. This options can also be specified through the
    environment variable IPYTHONDIR.
--writer=<DottedObjectName> (NbConvertApp.writer_class)
    Default: 'FilesWriter'
    Writer class used to write the  results of the conversion
--log-level=<Enum> (Application.log_level)
    Default: 30
    Choices: (0, 10, 20, 30, 40, 50, 'DEBUG', 'INFO', 'WARN', 'ERROR', 'CRITICAL')
    Set the log level by value or name.
--to=<CaselessStrEnum> (NbConvertApp.export_format)
    Default: 'html'
    Choices: ['custom', 'html', 'latex', 'markdown', 'python', 'rst', 'slides']
    The export format to be used.
--template=<Unicode> (Exporter.template_file)
    Default: u'default'
    Name of the template file to use
--output=<Unicode> (NbConvertApp.output_base)
    Default: ''
    overwrite base name use for output files. can only  be use when converting
    one notebook at a time.
--post=<DottedOrNone> (NbConvertApp.post_processor_class)
    Default: u''
    PostProcessor class used to write the  results of the conversion
--config=<Unicode> (BaseIPythonApplication.extra_config_file)
    Default: u''
    Path to an extra config file to load.
    If specified, load this config file in addition to any other IPython config.
--profile-dir=<Unicode> (ProfileDir.location)
    Default: u''
    Set the profile location directly. This overrides the logic used by the
    `profile` option.

To see all available configurables, use `--help-all`

Examples
--------

    The simplest way to use nbconvert is
    
    > ipython nbconvert mynotebook.ipynb
    
    which will convert mynotebook.ipynb to the default format (probably HTML).
    
    You can specify the export format with `--to`.
    Options include ['custom', 'html', 'latex', 'markdown', 'python', 'rst', 'slides']
    
    > ipython nbconvert --to latex mynotebook.ipnynb
    
    Both HTML and LaTeX support multiple output templates. LaTeX includes
    'basic', 'book', and 'article'.  HTML includes 'basic' and 'full'.  You 
    can specify the flavor of the format used.
    
    > ipython nbconvert --to html --template basic mynotebook.ipynb
    
    You can also pipe the output to stdout, rather than a file
    
    > ipython nbconvert mynotebook.ipynb --stdout
    
    A post-processor can be used to compile a PDF
    
    > ipython nbconvert mynotebook.ipynb --to latex --post PDF
    
    You can get (and serve) a Reveal.js-powered slideshow
    
    > ipython nbconvert myslides.ipynb --to slides --post serve
    
    Multiple notebooks can be given at the command line in a couple of 
    different ways:
    
    > ipython nbconvert notebook*.ipynb
    > ipython nbconvert notebook1.ipynb notebook2.ipynb
    
    or you can specify the notebooks list in a config file, containing::
    
        c.NbConvertApp.notebooks = ["my_notebook.ipynb"]
    
    > ipython nbconvert --config mycfg.py


In []: