dammit
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dib-lab
Install instructions for Ubuntu
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
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
Any reason the native Ubuntu package for Transdecoder isn't being used?
http://packages.ubuntu.com/search?keywords=transdecoder
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)
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.
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.
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.
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 <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
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 .
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 https://github.com/camillescott/dammit/issues/9#issuecomment-163774776.
Camille Scott
Department of Computer Science Lab for Data Intensive Biology University of California, Davis