I'm going to concatonate the Sept and Nov runs from my Larvae data (R1 and R2 separately)

F_R1

In [1]: 
!cat /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Nov/filtered_BS_CgF_TTAGGC_L004_R1.fastq /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Sept/filtered_BS_CgF_TTAGGC_L007_R1.fastq > /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/F_R1.fastq

M1_R1

In [2]: 
!cat /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Nov/filtered_BS_CgM1_ACTTGA_L004_R1.fastq /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Sept/filtered_BS_CgM1_ACTTGA_L007_R1.fastq > /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M1_R1.fastq

M3_R1

In [3]: 
!cat /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Nov/filtered_BS_CgM3_GATCAG_L004_R1.fastq /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Sept/filtered_BS_CgM3_GATCAG_L007_R1.fastq > /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M3_R1.fastq

T1D3_R1

In [4]: 
!cat /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Nov/filtered_BS_CgLarv_T1D3_TGACCA_L004_R1.fastq /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Sept/filtered_BS_CgLarv_T1D3_TGACCA_L007_R1.fastq > /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D3_R1.fastq

T1D5_R1

In [5]: 
!cat /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Nov/filtered_BS_CgLarv_T1D5_ACAGTG_L004_R1.fastq /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Sept/filtered_BS_CgLarv_T1D5_ACAGTG_L007_R1.fastq >  /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D5_R1.fastq

T3D3_R1

In [6]: 
!cat /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Nov/filtered_Bs_CgLarve_T3D3_GCCAAT_L004_R1.fastq /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Sept/filtered_Bs_CgLarve_T3D3_GCCAAT_L007_R1.fastq > /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D3_R1.fastq

T3D5_R1

In [7]: 
!cat /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Nov/filtered_BS_CgLarv_T3D5_CAGATC_L004_R1.fastq /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Sept/filtered_BS_CgLarv_T3D5_CAGATC_L007_R1.fastq > /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D5_R1.fastq

F_R2

In [8]: 
!cat /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Nov/filtered_BS_CgF_TTAGGC_L004_R2.fastq /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Sept/filtered_BS_CgF_TTAGGC_L007_R2.fastq > /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/F_R2.fastq

M1_R2

In [9]: 
!cat /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Nov/filtered_BS_CgM1_ACTTGA_L004_R2.fastq /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Sept/filtered_BS_CgM1_ACTTGA_L007_R2.fastq > /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/M1_R2.fastq

M3_R2

In [10]: 
!cat /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Nov/filtered_BS_CgM3_GATCAG_L004_R2.fastq /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Sept/filtered_BS_CgM3_GATCAG_L007_R2.fastq >  /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/M3_R2.fastq

T1D3_R2

In [11]: 
!cat /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Nov/filtered_BS_CgLarv_T1D3_TGACCA_L004_R2.fastq /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Sept/filtered_BS_CgLarv_T1D3_TGACCA_L007_R2.fastq >  /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T1D3_R2.fastq

T1D5_R2

In [12]: 
!cat /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Nov/filtered_BS_CgLarv_T1D5_ACAGTG_L004_R2.fastq /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Sept/filtered_BS_CgLarv_T1D5_ACAGTG_L007_R2.fastq > /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T1D5_R2.fastq

T3D3_R2

In [13]: 
!cat /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Nov/filtered_Bs_CgLarve_T3D3_GCCAAT_L004_R2.fastq /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Sept/filtered_Bs_CgLarve_T3D3_GCCAAT_L007_R2.fastq > /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T3D3_R2.fastq

T3D5_R2

In [14]: 
!cat /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Nov/filtered_BS_CgLarv_T3D5_CAGATC_L004_R2.fastq /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Sept/filtered_BS_CgLarv_T3D5_CAGATC_L007_R2.fastq > /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T3D5_R2.fastq

Script to take html snapshot of IPython notebook

Notes from Steven's notebook: http://nbviewer.ipython.org/urls/dl.dropboxusercontent.com/u/115356/ip/nbview/_IPsnapshot.ipynb
In [4]: 
#NOTEBOOK NAME
nb='Concatenate_Larvae_Files'

#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_Posts/'
In [5]: 
cd {post}

/Volumes/web/Mollusk/iPython_Posts
In [6]: 
!ipython nbconvert {nbloc}{nb} --to html --template full --output {nb}{date}

[NbConvertApp] Using existing profile dir: u'/Users/claireolson/.ipython/profile_default'
[NbConvertApp] Converting notebook /Users/claireolson/Dropbox/Lab (1)/IPython_nbs/Claire/Concatenate_Larvae_Files.ipynb to html
[NbConvertApp] Support files will be in Concatenate_Larvae_Files[0331_1042]_files/
[NbConvertApp] Loaded template html_full.tpl
[NbConvertApp] ERROR | Error while converting '/Users/claireolson/Dropbox/Lab (1)/IPython_nbs/Claire/Concatenate_Larvae_Files.ipynb'
Traceback (most recent call last):
  File "/Users/claireolson/anaconda/lib/python2.7/site-packages/IPython/nbconvert/nbconvertapp.py", line 300, in convert_notebooks
    output, resources = exporter.from_filename(notebook_filename, resources=resources)
  File "/Users/claireolson/anaconda/lib/python2.7/site-packages/IPython/nbconvert/exporters/exporter.py", line 289, in from_filename
    return self.from_notebook_node(nbformat.read(f, 'json'), resources=resources,**kw)
  File "/Users/claireolson/anaconda/lib/python2.7/site-packages/IPython/nbconvert/exporters/exporter.py", line 260, in from_notebook_node
    output = self.template.render(nb=nb_copy, resources=resources)
  File "/Users/claireolson/anaconda/lib/python2.7/site-packages/jinja2/environment.py", line 969, in render
    return self.environment.handle_exception(exc_info, True)
  File "/Users/claireolson/anaconda/lib/python2.7/site-packages/jinja2/environment.py", line 742, in handle_exception
    reraise(exc_type, exc_value, tb)
  File "/Users/claireolson/anaconda/lib/python2.7/site-packages/IPython/nbconvert/exporters/../templates/html_full.tpl", line 1, in top-level template code
    {%- extends 'html_basic.tpl' -%}
  File "/Users/claireolson/anaconda/lib/python2.7/site-packages/IPython/nbconvert/exporters/../templates/html_basic.tpl", line 1, in top-level template code
    {%- extends 'display_priority.tpl' -%}
  File "/Users/claireolson/anaconda/lib/python2.7/site-packages/IPython/nbconvert/exporters/../templates/skeleton/display_priority.tpl", line 1, in top-level template code
    {%- extends 'null.tpl' -%}
  File "/Users/claireolson/anaconda/lib/python2.7/site-packages/IPython/nbconvert/exporters/../templates/skeleton/null.tpl", line 26, in top-level template code
    {%- block body -%}
  File "/Users/claireolson/anaconda/lib/python2.7/site-packages/IPython/nbconvert/exporters/../templates/html_full.tpl", line 62, in block "body"
    {{ super() }}
  File "/Users/claireolson/anaconda/lib/python2.7/site-packages/IPython/nbconvert/exporters/../templates/skeleton/null.tpl", line 29, in block "body"
    {%- block any_cell scoped -%}
  File "/Users/claireolson/anaconda/lib/python2.7/site-packages/IPython/nbconvert/exporters/../templates/skeleton/null.tpl", line 76, in block "any_cell"
    {%- block headingcell scoped-%}
  File "/Users/claireolson/anaconda/lib/python2.7/site-packages/IPython/nbconvert/exporters/../templates/html_basic.tpl", line 64, in block "headingcell"
    {{ ("#" * cell.level + cell.source) | replace('\n', ' ') | strip_math_space | markdown2html | strip_files_prefix | add_anchor }}
  File "/Users/claireolson/anaconda/lib/python2.7/site-packages/IPython/nbconvert/filters/markdown.py", line 55, in markdown2html
    return pandoc(source, 'markdown', 'html', extra_args=['--mathjax'])
  File "/Users/claireolson/anaconda/lib/python2.7/site-packages/IPython/nbconvert/utils/pandoc.py", line 64, in pandoc
    "http://johnmacfarlane.net/pandoc/installing.html"
PandocMissing: The command 'pandoc -f markdown -t html --mathjax' returned an error: [Errno 2] No such file or directory.
Please check that pandoc is installed:
http://johnmacfarlane.net/pandoc/installing.html
In []: