Installation issues with hmmer2
2
0
Entering edit mode
7.3 years ago
JV ▴ 440

Hi everyone,

I want to use rnammer with my favorite annotation pipeline prokka (as a supposedly more sensitive option than the default-tool barnap). The prokka documentation states that rnammer needs hmmer version 2 (NOT the current version 3), so I want to install it on my system.

The Installation-instructions seem pretty straightforward (unpack--> "make check"-->"./configure"-->"make install").

However when I run "make check", I get the message :

make: *** No rule to make target 'check';. Stop.

when I run "./configure --prefix=/home/me/test" the script seems to run without error, but when i follow up with "make install" I get the message:

mkdir -p /home/me/test/bin
mkdir -p /home/me/test/man/man1
for file in hmmalign hmmbuild hmmcalibrate hmmconvert hmmemit hmmfetch hmmindex hmmpfam hmmsearch
  do
  cp src/$file /home/me/test/bin/
  done



cp: cannot stat 'src/hmmalign': No such file or directory
cp: cannot stat 'src/hmmbuild': No such file or directory
cp: cannot stat 'src/hmmcalibrate': No such file or directory
cp: cannot stat 'src/hmmconvert': No such file or directory
cp: cannot stat 'src/hmmemit': No such file or directory
cp: cannot stat 'src/hmmfetch': No such file or directory
cp: cannot stat 'src/hmmindex': No such file or directory
cp: cannot stat 'src/hmmpfam': No such file or directory
cp: cannot stat 'src/hmmsearch': No such file or directory
make: *** [install] Error 1

This happens with or without the configure-option '--prefix' and with or without admin rights.

Any hints on what to do?

hmmer hmmer2 hmmsearch prokka • 3.5k views
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0
Entering edit mode

Hello JV!

We believe that this post does not fit the main topic of this site.

problem solved

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

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3
Entering edit mode
7.3 years ago
Ram 35k

Hi,

I see the installation instructions go:

curl -O ftp://selab.janelia.org/pub/software/hmmer/2.3.2/hmmer-2.3.2.tar.gz
tar -xzf hmmer-2.3.2.tar.gz
cd hmmer-2.3.2
./configure
make
make check

That should work, it does for me.

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0
Entering edit mode
7.3 years ago
JV ▴ 440

Yes, that was it!

I had went with the instructions for the binary version by mistake. So no wonder it did not work (Stupid me!).

Your instructions (for the src-version) work perfectly.

Thanks!

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0
Entering edit mode

Hi,

Glad it helped. Could you maybe accept my answer please? And I'm confused why you closed your own post using a moderation edit instead of accepting an answer :)

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1
Entering edit mode

Sorry, wasn't sure how this worked. I had already upvoted your answer and thought closing the thread as "solved" would be the thing to do.

I marked your answer as accepted now.

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0
Entering edit mode

Thank you.  Yeah, moderation --> close is for when you wanna bypass the Q&A workflow and mark a question outside the scope of the forum. The usual workflow is ask --> choose one or more of the answers as the accepted answer(s). Can be kinda confusing at times, I guess.

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