I'm not being able to use TransDecoder because of URI::Escape module, but it's already installed #174
Comments
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Hi,
I'd suggest trying the latest version:
https://github.com/TransDecoder/TransDecoder/releases/tag/TransDecoder-v5.7.0
I don't think it should need the URI::Escape anymore, but let me know if it
still gives you trouble.
best,
~b
…On Fri, Apr 28, 2023 at 12:24 PM Vinícius Castro Santos < ***@***.***> wrote:
I'm trying to use TransDecoder, but I'm getting this error:
TransDecoder.LongOrfs -h
Can't locate URI/Escape.pm in @inc <https://github.com/inc> (you may need
to install the URI::Escape module) ***@***.*** <https://github.com/inc>
contains: /opt/anaconda3/opt/transdecoder/PerlLib
/opt/anaconda3/lib/site_perl/5.34.0/x86_64-linux-thread-multi
/opt/anaconda3/lib/site_perl/5.34.0
/opt/anaconda3/lib/5.34.0/x86_64-linux-thread-multi
/opt/anaconda3/lib/5.34.0 .) at
/opt/anaconda3/opt/transdecoder/PerlLib/Gene_obj.pm line 15. BEGIN
failed--compilation aborted at
/opt/anaconda3/opt/transdecoder/PerlLib/Gene_obj.pm line 15. Compilation
failed in require at /opt/anaconda3/bin/TransDecoder.LongOrfs line 64.
BEGIN failed--compilation aborted at
/opt/anaconda3/bin/TransDecoder.LongOrfs line 64.
But URI::Escape is already installed!
sudo cpanm install URI::Escape
install is up to date. (0.01) URI::Escape is up to date. (5.17)
It would be expected to work perfectly after installing the dependencies,
but unfortunately, it is not working as expected. I even tried to reboot
the server, but it didn't make any difference.
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Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>
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I tried to install TransDecoder from source using the 'make' command as instructed: 'The latest release of TransDecoder can be found here. Run 'make' in the base installation directory.' However, I encountered an error within the TransDecoder-TransDecoder-v5.7.0 directory:
So, I had to use bioconda, but the version is to old. I tried to specify the version to 5.7.0, which is said to be available in bioconda channel.
Name Version Build Channeltransdecoder 2.1.0 0 bioconda However, when I tried do download it, the bioconda/linux-64::transdecoder-2.1.0-0 is being downloaded :
Solving environment: failed with initial frozen solve. Retrying with flexible solve. Package Planenvironment location: /opt/anaconda3 added / updated specs: The following packages will be downloaded: The following NEW packages will be INSTALLED: libgcc conda-forge/linux-64::libgcc-7.2.0-h69d50b8_2 Proceed ([y]/n)? y Downloading and Extracting Packages Preparing transaction: done |
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hi,
Try just pulling the code down directly instead of using conda:
https://github.com/TransDecoder/TransDecoder/releases/tag/TransDecoder-v5.7.0
…On Fri, Apr 28, 2023 at 5:19 PM Vinícius Castro Santos < ***@***.***> wrote:
I tried to install TransDecoder from source using the 'make' command as
instructed: 'The latest release of TransDecoder can be found here. Run
'make' in the base installation directory.' However, I encountered an error
within the TransDecoder-TransDecoder-v5.7.0 directory:
Nothing to build. Run 'make test' to run example executions on each of the
sample data sets provided.
So, I had to use bioconda, but the version is to old. I tryed to specify
the version to 5.7.0, which is said be available in bioconda channel.
conda search transdecoder
`
Name Version Build Channel
transdecoder 2.1.0 0 bioconda
transdecoder 2.1.0 1 bioconda
transdecoder 2.1.0 2 bioconda
transdecoder 2.1.0 3 bioconda
transdecoder 2.1.0 4 bioconda
transdecoder 2.1.0 5 bioconda
transdecoder 3.0.1 0 bioconda
transdecoder 3.0.1 1 bioconda
transdecoder 3.0.1 2 bioconda
transdecoder 3.0.1 pl5.22.0_0 bioconda
transdecoder 5.0.2 pl5.22.0_0 bioconda
transdecoder 5.1.0 pl5.22.0_0 bioconda
transdecoder 5.2.0 pl5.22.0_0 bioconda
transdecoder 5.3.0 0 bioconda
transdecoder 5.5.0 0 bioconda
transdecoder 5.5.0 pl5262hdfd78af_4 bioconda
transdecoder 5.5.0 pl526_1 bioconda
transdecoder 5.5.0 pl526_2 bioconda
transdecoder 5.5.0 pl526_3 bioconda
transdecoder 5.5.0 pl5321hdfd78af_5 bioconda
transdecoder 5.7.0 pl5321hdfd78af_0 bioconda
`
However, when I tried do download it, the
bioconda/linux-64::transdecoder-2.1.0-0 is being downloaded :
conda install -c bioconda transdecoder=5.7.0
Solving environment: failed with initial frozen solve. Retrying with
flexible solve.
Solving environment: failed with repodata from current_repodata.json, will
retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: done
Package Plan
environment location: /opt/anaconda3
added / updated specs:
- transdecoder
The following packages will be downloaded:
package | build
---------------------------|-----------------
libgcc-7.2.0 | h69d50b8_2 304 KB conda-forge
------------------------------------------------------------
Total: 304 KB
The following NEW packages will be INSTALLED:
libgcc conda-forge/linux-64::libgcc-7.2.0-h69d50b8_2
transdecoder bioconda/linux-64::transdecoder-2.1.0-0
Proceed ([y]/n)? y
Downloading and Extracting Packages
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
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Brian J. Haas
The Broad Institute
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Hi, Brian! I've done that, but for some reason when I use 'make' within the TransDecoder-v5.7.0 directory, I'm getting this:
And in the instructions is written: 'The latest release of TransDecoder can be found here [https://github.com/TransDecoder/TransDecoder/releases/tag/TransDecoder-v5.7.0]. Run 'make' in the base installation directory.' |
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Ah - I see. Right, no need to run 'make'. I just updated the
documentation. Should be good to go.
best,
~b
…On Fri, Apr 28, 2023 at 6:33 PM Vinícius Castro Santos < ***@***.***> wrote:
Hi, Brian! I've done that, but for some reason when I use 'make' within
the TransDecoder-v5.7.0 directory, I'm getting this:
Nothing to build. Run 'make test' to run example executions on each of the
sample data sets provided.
And in the instructions is written:
'The latest release of TransDecoder can be found here [
https://github.com/TransDecoder/TransDecoder/releases/tag/TransDecoder-v5.7.0].
Run 'make' in the base installation directory.'
—
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<#174 (comment)>,
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Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>
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Oh, great! Thank you very much, Brian! |
I'm trying to use TransDecoder, but I'm getting this error:
TransDecoder.LongOrfs -hCan't locate URI/Escape.pm in @inc (you may need to install the URI::Escape module) (@inc contains: /opt/anaconda3/opt/transdecoder/PerlLib /opt/anaconda3/lib/site_perl/5.34.0/x86_64-linux-thread-multi /opt/anaconda3/lib/site_perl/5.34.0 /opt/anaconda3/lib/5.34.0/x86_64-linux-thread-multi /opt/anaconda3/lib/5.34.0 .) at /opt/anaconda3/opt/transdecoder/PerlLib/Gene_obj.pm line 15. BEGIN failed--compilation aborted at /opt/anaconda3/opt/transdecoder/PerlLib/Gene_obj.pm line 15. Compilation failed in require at /opt/anaconda3/bin/TransDecoder.LongOrfs line 64. BEGIN failed--compilation aborted at /opt/anaconda3/bin/TransDecoder.LongOrfs line 64.
But URI::Escape is already installed!
sudo cpanm install URI::Escapeinstall is up to date. (0.01) URI::Escape is up to date. (5.17)
It would be expected to work perfectly after installing the dependencies, but unfortunately, it is not working as expected. I even tried to reboot the server, but it didn't make any difference.
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