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dib-lab / dammit

just annotate it, dammit!
http://dib-lab.github.io/dammit/
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Install instructions for Ubuntu #9

Open ctb opened 9 years ago

ctb commented 9 years ago 
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 commented 9 years ago

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

ctb commented 9 years ago

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

ctb commented 9 years ago

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 commented 9 years ago

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

mr-c commented 8 years ago

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

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

mr-c commented 8 years ago

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 commented 8 years ago

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 commented 8 years ago

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 notifications@github.com 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.

mr-c commented 8 years ago

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

On Fri, Dec 11, 2015, 00:36 Michael Crusoe michael.crusoe@gmail.com 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 notifications@github.com 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.

camillescott commented 8 years ago

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 <notifications@github.com

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 michael.crusoe@gmail.com 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 notifications@github.com 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 https://github.com/camillescott/dammit/issues/9#issuecomment-163773583.

Camille Scott

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

camille.scott.w@gmail.com

mr-c commented 8 years ago

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 michael.crusoe@gmail.com 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 michael.crusoe@gmail.com 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 notifications@github.com 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 .

camillescott commented 8 years ago

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 <notifications@github.com

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 michael.crusoe@gmail.com 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 michael.crusoe@gmail.com 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 notifications@github.com 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 https://github.com/camillescott/dammit/issues/9#issuecomment-163774776.

Camille Scott

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

camille.scott.w@gmail.com