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AWS ami information |
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June 11th, 2015 |
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{% include JB/setup %}
Our AWS ami can be found by searching for EDAMAME-2015 or ami-af04f2c4. See this page for help on finding public AMIs.
Here's what on the AMI and everything should be playing well together:
Everyday packages installed from scratch: R (only extras are base packages used by QIIME & mothur) abyss aragorn autoconf automake bamtools barrnap bedtools bio-awk biom bison blast boost bowtie bwa bzip2 cmake curl expat gcc gmp google-sparsehash hmmer htslib infernal isl jpeg libmpc libpng libtool makedepend megahit mpfr openssl parallel pcre pkg-config prodigal prokka quast samtools seqtk spades tbl2asn tcl-tk trinity velvet xz
Python Packages alabaster==0.7.4 awscli==1.7.32 Babel==1.3 backports.ssl-match-hostname==3.4.0.2 BamM==1.4.1 bcdoc==0.15.0 biom-format==2.1.4 botocore==1.0.0b1 burrito-fillings==0.1.1 burrito==0.9.1 bz2file==0.98 certifi==2015.4.28 Cheetah==2.4.4 cogent==1.5.3 colorama==0.3.3 Cython==0.22 docutils==0.12 dumbo==0.21.35 emperor==0.9.51 future==0.14.3 gdata==2.0.18 GnuPGInterface==0.3.2 ipython==3.1.0 Jinja2==2.7.3 jmespath==0.7.1 lazr.uri==1.0.3 Markdown==2.6.2 MarkupSafe==0.23 matplotlib==1.4.3 mock==1.0.1 natsort==3.5.6 nose==1.3.7 numexpr==2.4.3 numpy==1.9.2 numpydoc==0.5 oauth==1.0.1 PAM==0.4.2 pandas==0.16.1 PrimerProspector===1.0.1-release pyasn1==0.1.7 pyfasta==0.5.2 Pygments==2.0.2 pynast==1.2.2 pyparsing==2.0.3 pyqi==0.3.2 python-apt===0.8.3ubuntu7.3 python-dateutil==2.4.2 pytz==2015.4 qcli==0.1.1 qiime-default-reference==0.1.3 qiime==1.9.1 rsa==3.1.4 scikit-bio==0.2.3 scikits.statsmodels==0.3.1 scipy==0.15.1 screed==0.8 six==1.9.0 snowballstemmer==1.2.0 sphinx-rtd-theme==0.1.8 Sphinx==1.3.1 tax2tree==1.0 Twisted-Core==11.1.0 typedbytes==0.3.8 ufw==0.31.1.post1
1450 Perl Packages (not going to list them here -- ask me if you can't find something and I will point you in the right direction)
Please test the AMI with your tutorials and data and if you run into any errors, please open an issue.
When you open the issue, please provide me with two things:
- The exact code you ran that gave you the error
- The response to the screen that you received
Those things will help me to fix any problems. Thanks! ~ josh