Install instructions for Ubuntu

[ctb]

apt-get update
apt-get -y install python-pip python-dev python-numpy git ruby \
   liburi-escape-xs-perl emboss liburi-perl

pip install -U setuptools

[ctb]

Also, run 'make' in Transdecoder, and use TransDecoder 2.0 (?)

[ctb]

(the --cpu option needs to be removed for Transdecoder 2.0.1)

[ctb]

More explicit:

sudo apt-get update &&
sudo apt-get -y install python-pip python-dev python-numpy git ruby \
   liburi-escape-xs-perl emboss liburi-perl  \
   python-pip python-dev python-numpy git ruby hmmer \
    infernal ncbi-blast+ liburi-escape-xs-perl emboss liburi-perl unzip

sudo pip install -U setuptools

cd
wget https://github.com/TransDecoder/TransDecoder/archive/2.0.1.tar.gz
tar -xvzf 2.0.1.tar.gz
cd TransDecoder-2.0.1; make
export PATH=$PATH:$HOME/TransDecoder-2.0.1
echo 'export PATH=$PATH:$HOME/TransDecoder-2.0.1' >> $HOME/.bashrc

sudo gem install crb-blast

cd
wget http://last.cbrc.jp/last-658.zip
unzip last-658.zip
cd last-658
sudo make install

cd
wget http://busco.ezlab.org/files/BUSCO_v1.1b1.tar.gz
tar -xvzf BUSCO_v1.1b1.tar.gz
chmod +x BUSCO_v1.1b1/BUSCO_v1.1b1.py
export PATH=$PATH:$HOME/BUSCO_v1.1b1

echo 'export PATH=$PATH:$HOME/BUSCO_v1.1b1' >> $HOME/.bashrc

sudo pip install dammit

[ctb]

(This needs the fixes in #13 to actually run, though.)

[mr-c]

Any reason the native Ubuntu package for Transdecoder isn't being used?

http://packages.ubuntu.com/search?keywords=transdecoder

[mr-c]

Also, I can backport last version 658 from Ubuntu Xenial to all the current LTS releases if you'd like.

http://packages.ubuntu.com/search?keywords=last-align

(FYI: if you are installing from stock Ubuntu then you are just using the Ubuntu archive; not a PPA (personal pick archive) as stated in the README)

[camillescott]

Ahh, I hadn't realized TransDecoder had made it into backports. It also looks like the EC2 14.04 images don't have backports enabled by default (and neither did my system), which requires users to edit their sources.list. I'll look at add that option to the instructions.

[mr-c]

That's odd, I thought backports were enabled by default.

"First, you must ensure that apt is configured with Backports enabled. On
releases after and including Ubuntu 11.10 (Oneiric Ocelot), this is not
necessary, as apt is configured with Backports enabled by default." First,
you must ensure that apt is configured with Backports enabled. On releases
after and including Ubuntu 11.10 (Oneiric Ocelot), this is not necessary,
as apt is configured with Backports enabled by default.

On Thu, Dec 10, 2015, 23:25 Camille Scott [email protected] wrote:

Ahh, I hadn't realized TransDecoder had made it into backports. It also
looks like the EC2 14.04 images don't have backports enabled by default
(and neither did my system), which requires users to edit their
sources.list. I'll look at add that option to the instructions.

—
Reply to this email directly or view it on GitHub
#9 (comment).

[mr-c]

Please pretend that second paste was a link to
https://help.ubuntu.com/community/UbuntuBackports

On Fri, Dec 11, 2015, 00:36 Michael Crusoe [email protected] wrote:

That's odd, I thought backports were enabled by default.

"First, you must ensure that apt is configured with Backports enabled. On
releases after and including Ubuntu 11.10 (Oneiric Ocelot), this is not
necessary, as apt is configured with Backports enabled by default." First,
you must ensure that apt is configured with Backports enabled. On releases
after and including Ubuntu 11.10 (Oneiric Ocelot), this is not necessary,
as apt is configured with Backports enabled by default.

On Thu, Dec 10, 2015, 23:25 Camille Scott [email protected]
wrote:

Ahh, I hadn't realized TransDecoder had made it into backports. It also
looks like the EC2 14.04 images don't have backports enabled by default
(and neither did my system), which requires users to edit their
sources.list. I'll look at add that option to the instructions.

—
Reply to this email directly or view it on GitHub
#9 (comment).

[camillescott]

The documentation does indeed say they are enabled by default, but on the
images supplied by Amazon for a "bare" 14.04 they are commented out. I
believe the same held true for my last Ubuntu install as well.

On Thu, Dec 10, 2015 at 2:37 PM, Michael R. Crusoe <[email protected]

wrote:

Please pretend that second paste was a link to
https://help.ubuntu.com/community/UbuntuBackports

On Fri, Dec 11, 2015, 00:36 Michael Crusoe [email protected]
wrote:

That's odd, I thought backports were enabled by default.

"First, you must ensure that apt is configured with Backports enabled. On
releases after and including Ubuntu 11.10 (Oneiric Ocelot), this is not
necessary, as apt is configured with Backports enabled by default."
First,
you must ensure that apt is configured with Backports enabled. On
releases
after and including Ubuntu 11.10 (Oneiric Ocelot), this is not necessary,
as apt is configured with Backports enabled by default.

On Thu, Dec 10, 2015, 23:25 Camille Scott [email protected]
wrote:

Ahh, I hadn't realized TransDecoder had made it into backports. It also
looks like the EC2 14.04 images don't have backports enabled by default
(and neither did my system), which requires users to edit their
sources.list. I'll look at add that option to the instructions.

—
Reply to this email directly or view it on GitHub
<#9 (comment)
.

—
Reply to this email directly or view it on GitHub
#9 (comment).

Camille Scott

Department of Computer Science
Lab for Data Intensive Biology
University of California, Davis

[email protected]

[mr-c]

Here's a oneliner

sudo add-apt-repository "deb http://archive.ubuntu.com/ubuntu
trusty-backports main restricted universe multiverse"

On Fri, Dec 11, 2015, 00:37 Michael Crusoe [email protected] wrote:

Please pretend that second paste was a link to
https://help.ubuntu.com/community/UbuntuBackports

On Fri, Dec 11, 2015, 00:36 Michael Crusoe [email protected]
wrote:

That's odd, I thought backports were enabled by default.

"First, you must ensure that apt is configured with Backports enabled. On
releases after and including Ubuntu 11.10 (Oneiric Ocelot), this is not
necessary, as apt is configured with Backports enabled by default." First,
you must ensure that apt is configured with Backports enabled. On releases
after and including Ubuntu 11.10 (Oneiric Ocelot), this is not necessary,
as apt is configured with Backports enabled by default.

On Thu, Dec 10, 2015, 23:25 Camille Scott [email protected]
wrote:

Ahh, I hadn't realized TransDecoder had made it into backports. It also
looks like the EC2 14.04 images don't have backports enabled by default
(and neither did my system), which requires users to edit their
sources.list. I'll look at add that option to the instructions.

—
Reply to this email directly or view it on GitHub
#9 (comment)
.

[camillescott]

Now that I like. I'll get it added into the install instructions.

On Thu, Dec 10, 2015 at 2:39 PM, Michael R. Crusoe <[email protected]

wrote:

Here's a oneliner

sudo add-apt-repository "deb http://archive.ubuntu.com/ubuntu
trusty-backports main restricted universe multiverse"

On Fri, Dec 11, 2015, 00:37 Michael Crusoe [email protected]
wrote:

Please pretend that second paste was a link to
https://help.ubuntu.com/community/UbuntuBackports

On Fri, Dec 11, 2015, 00:36 Michael Crusoe [email protected]
wrote:

That's odd, I thought backports were enabled by default.

"First, you must ensure that apt is configured with Backports enabled.
On
releases after and including Ubuntu 11.10 (Oneiric Ocelot), this is not
necessary, as apt is configured with Backports enabled by default."
First,
you must ensure that apt is configured with Backports enabled. On
releases
after and including Ubuntu 11.10 (Oneiric Ocelot), this is not
necessary,
as apt is configured with Backports enabled by default.

On Thu, Dec 10, 2015, 23:25 Camille Scott [email protected]
wrote:

Ahh, I hadn't realized TransDecoder had made it into backports. It also
looks like the EC2 14.04 images don't have backports enabled by default
(and neither did my system), which requires users to edit their
sources.list. I'll look at add that option to the instructions.

—
Reply to this email directly or view it on GitHub
<
https://github.com/camillescott/dammit/issues/9#issuecomment-163753873>
.

—
Reply to this email directly or view it on GitHub
#9 (comment).

Camille Scott

Department of Computer Science
Lab for Data Intensive Biology
University of California, Davis

[email protected]