TransDecoder

TransDecoder

github
latest release

Install

By Bioconda

conda install -c bioconda transdecoder 

Build from Source

Downloading the file and make a test (16M)

wget -c https://github.com/TransDecoder/TransDecoder/archive/TransDecoder-v5.5.0.tar.gz
tar -zxvf TransDecoder-v5.5.0.tar.gz
cd TransDecoder-TransDecoder-v5.5.0/
make test

You are supposed to see the code below after execute make test

-Fasta_retriever:: begin initializing for supertranscripts.fasta
-Fasta_retriever:: done initializing for supertranscripts.fasta

+ echo Done
Done
make[2]: Leaving directory '/home/ken/Bio/TransDecoder-TransDecoder-v5.5.0/sample_data/supertranscripts_example'
make[1]: Leaving directory '/home/ken/Bio/TransDecoder-TransDecoder-v5.5.0/sample_data'

If it comes with any Error during the make test,

please see the ‘Debug’ at the end.

Now, add the current directory to your $PATH:

echo -e "\n#TransDecoder\n export PATH=\$PATH:$(pwd)" >> ~/.bashrc
source  ~/.bashrc

So, it will add the line below to the end of the ~/.bashrc file.

##TransDecoder
 export PATH=$PATH:/home/ken/Bio/TransDecoder-TransDecoder-v5.5.0

Now, you can ENJOY the TransDecoder.

Running TransDecoder

Preparing a fasta file as HitMe.fa

Extract the long open reading frames

TransDecoder.LongOrfs -t HitMe.fa

The result should be the longest_orfs.pep

Debug

E1; makeblastdb: command not found

code

./runMe.sh: line 49: makeblastdb: command not found
make[2]: *** [Makefile:2: test] Error 127
make[2]: Leaving directory '/home/ken/Bio/TransDecoder-TransDecoder-v5.5.0/sample_data/cufflinks_example'
make[1]: *** [Makefile:5: test] Error 2
make[1]: Leaving directory '/home/ken/Bio/TransDecoder-TransDecoder-v5.5.0/sample_data'
make: *** [Makefile:10: test] Error 2

./runMe.sh: line 49: makeblastdb: command not found

Why&How

Lake of blast+

sudo apt-get install ncbi-blast+

E2; hmmpress: command not found

code

./runMe.sh: line 56: hmmpress: command not found
make[2]: *** [Makefile:2: test] Error 127
make[2]: Leaving directory '/home/ken/Bio/TransDecoder-TransDecoder-v5.5.0/sample_data/cufflinks_example'
make[1]: *** [Makefile:5: test] Error 2
make[1]: Leaving directory '/home/ken/Bio/TransDecoder-TransDecoder-v5.5.0/sample_data'
make: *** [Makefile:10: test] Error 2

Why&How

Lake of hammper2

sudo apt-get install hmmer