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SystemsBioinformatics / cbmpy-metadraft

CBMPy Metadraft: a flexible and extensible genome-scale model reconstruction tool
https://systemsbioinformatics.github.io/cbmpy-metadraft/
GNU General Public License v3.0
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Installation instruction of required Blast modules are missing in the README #11

Open willigott opened 3 years ago

willigott commented 3 years ago

When one follows the installation instructions of the README and tries to run a BLAST, one can end up with messages like this:


Starting first BLAST pass for IN - IN on 05/09/2021sh: 1: blastall: not found

no element found at line 1, column 0, byte -1 at ./blast_parser.pl line 110.

Starting second BLAST pass for IN - IN on 
Starting first BLAST pass for IN - DB on 05/09/202105/09/2021sh: 1: blastall: not found

no element found at line 1, column 0, byte -1 at ./blast_parser.pl line 110.

Starting second BLAST pass for IN - DB on 
Starting first BLAST pass for DB - IN on 05/09/202105/09/2021sh: 1: blastall: not found

no element found at line 1, column 0, byte -1 at ./blast_parser.pl line 110.

Starting second BLAST pass for DB - IN on 
Starting first BLAST pass for DB - DB on 05/09/202105/09/2021sh: 1: blastall: not found

no element found at line 1, column 0, byte -1 at ./blast_parser.pl line 110.

On a Linux system, one can easily solve it by installing the missing modules like this:

sudo apt-get install ncbi-blast+-legacy

Might be good to add it to the README (in case I overlooked it somewhere, my apologies for the noise).

AdityaVaze commented 3 years ago

Hello,

I am a MSc student currently trying to use Metadraft for my thesis, and I am encountering a similar issue. I installed BLAST as per the instructions on the NCBI website, including the environment variables, so BLAST commands work in the Command Prompt. However, when I execute systemtest.py while in the metadraft3 environment, the BLAST tests fail.

willigott commented 3 years ago

@AdityaVaze: On which operating system do you work? If on linux, you can try the command I gave above:

sudo apt-get install ncbi-blast+-legacy

which worked fine for me. The legacy part is important, so if you are on windows make sure to download and install it.

AdityaVaze commented 3 years ago

Ah, I had the most recent version installed instead. I installed legacy BLAST on Windows and now it passes the systemtest. Thank you!

Samdeman35 commented 1 year ago

Ah, I had the most recent version installed instead. I installed legacy BLAST on Windows and now it passes the systemtest. Thank you!

Hi, where have you been able to download this legacy version? I have been trying to get BLAST to work for MetaDraft forever, but I can't seem to get it to work on my windows