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TransDecoder

github
latest release

Install

Downloading the file and make a test (16M)

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

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

  1. -Fasta_retriever:: begin initializing for supertranscripts.fasta
  2. -Fasta_retriever:: done initializing for supertranscripts.fasta
  4. + echo Done
  5. Done
  6. make[2]: Leaving directory '/home/ken/Bio/TransDecoder-TransDecoder-v5.5.0/sample_data/supertranscripts_example'
  7. 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:

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

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

  2. ##TransDecoder
  3.  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

1 Extract the long open reading frames

  1. TransDecoder.LongOrfs -t HitMe.fa

Debug

E1; makeblastdb: command not found

code

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

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

Why&How

Lake of blast+

  1. sudo apt-get install ncbi-blast+

E2; hmmpress: command not found

code

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

Why&How

Lake of hammper2

sudo apt-get install hammper2

Enjoy~

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由於語法渲染問題而影響閱讀體驗， 請移步博客閱讀～
本文GitPage地址

GitHub: Karobben
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