In [2]:

cd /usr/local/bioinformatics/

/usr/local/bioinformatics

In [3]:

#Download file (done outside of Jupyter, due to permission requirements)
!curl -O http://www.bioinformatics.babraham.ac.uk/projects/bismark/bismark_v0.14.2.tar.gz

  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0Warning: Failed to create the file bismark_v0.14.2.tar.gz: Permission denied
  0 1637k    0  1173    0     0   1479      0  0:18:53 --:--:--  0:18:53  1479
curl: (23) Failed writing body (0 != 1173)

In [1]:

#Unpack tarball (done outside of Jupyter, due to permission requirements)
!tar -zxvf bismark_v0.14.2.tar.gz

tar: Error opening archive: Failed to open 'bismark_v0.14.2.tar.gz'

In [4]:

cd /usr/local/bioinformatics/

/usr/local/bioinformatics

In [5]:

cd bismark_v0.14.2/

/usr/local/bioinformatics/bismark_v0.14.2

In [6]:

ls

Bismark_User_Guide.pdf         bismark_genome_preparation*
RELEASE_NOTES.txt              bismark_methylation_extractor*
RRBS_Guide.pdf                 bismark_sitrep.tpl
bismark*                       coverage2cytosine*
bismark2bedGraph*              deduplicate_bismark*
bismark2report*                license.txt

In [7]:

#add bismark to system PATH, via the /usr/local/bioinformatics/source.sh script
#added the following to the end of the source.sh script
## bismark
#export PATH=${BIO}/bismark_v0.14.2:${PATH}

In [1]:

#verify bismark is in PATH
!echo $PATH

/Users/Sam/anaconda/bin:/usr/local/bioinformatics/bismark_v0.14.2:/usr/local/bioinformatics/bedtools-2.22.1/bin:/usr/local/bioinformatics/cufflinks-2.2.1.OSX_x86_64:/usr/local/bioinformatics/FastQC:/usr/local/bioinformatics/tophat-2.0.13.OSX_x86_64:/usr/local/bioinformatics/signalp-4.1:/usr/local/bioinformatics/Trinotate:/usr/local/bioinformatics/ngsplot/bin:/usr/local/bioinformatics/stacks/bin:/usr/local/bioinformatics/rsem/sam:/usr/local/bioinformatics/fastx_toolkit/bin:/opt/local/Library/Frameworks/Python.framework/Versions/2.7/bin:/usr/local/bioinformatics/rsem:/usr/local/bioinformatics/bowtie2:/usr/local/bioinformatics/bowtie:/usr/local/bioinformatics/hmmer:/usr/local/bioinformatics/trinity:/usr/local/bioinformatics/ncbi-blast/bin:/usr/local/bioinformatics/anaconda/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin

In [ ]: