Error Makefile.PL

[ohan-Bioinfo]

Dear:

working with Mac operating system,

**echo "n" | cpanm -n  Data::Stag DB_File Bio::Root::Version Bio::SearchIO::blastxml Bio::SearchIO::hmmer**
Data::Stag is up to date. (0.14)
DB_File is up to date. (1.852)
Bio::Root::Version is up to date. (1.7.5)
Bio::SearchIO::blastxml is up to date. (1.70)
Bio::SearchIO::hmmer is up to date. (1.7.3)

  **cpanm --installdeps .**
--> Working on .
Configuring /Users/ohon_ad/Downloads/tephra-0.12.3 ... OK
<== Installed dependencies for .. Finishing.

 **perl Makefile.PL**
Generating a Unix-style Makefile
Writing Makefile for Tephra
Writing MYMETA.yml and MYMETA.json
=====> Configuring Tephra, this may take some time...rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
.util_lib.c:4:10: fatal error: 'malloc.h' file not found
#include <malloc.h>
         ^~~~~~~~~~
1 error generated.
make: *** [util_lib.o] Error 1
make failed: No such file or directory at lib/Tephra/Config/Install.pm line 726.

[sestaton]

It looks like you are missing the standard C library (glibc). Instead of working on the core libraries, which may be a challenge on Mac, can you try the Docker approach? That should work on Mac without any modifications.

Please let me know if you have issues with the commands in the README file.

[ohan-Bioinfo]

im still trying to compile and install it in my machine , has nothing to do with README yet
can you help to build this in my mac machine

[ohan-Bioinfo]

from Docker file

RUN apt-get update \
    && DEBIAN_FRONTEND=noninteractive apt-get install -y -qq \
    build-essential wget default-jre zlib1g-dev unzip libncurses5 libncurses5-dev libdb-dev git cpanminus libexpat1 libexpat1-dev libidn11 \

can't find those using brew or conda any suggestion?

[sestaton]

Hi, There is a Docker image on Docker Hub that I have built from the latest version. If you have Docker installed on your Mac (there is an installer on their website), then you can run the command using the suggestions from the README file. Specifically,

docker run -it --name tephra-con -v $(pwd)/db:/db:Z sestaton/tephra

That assumes you create a directory called "db" in the current working directory with all your analysis files (repeat DB, genome, config file, etc.). If you run that command it will mount the directory "db" at /db and attach you to a running container called "tephra-con" where you can run your analysis.

I would not recommend installing all those dependencies on your Mac system. If you don't want to use Docker, then start up a cloud Linux image and you can install Tephra with an install script in one go, but on Mac it is unsupported at this time (other than with Docker).

[ohan-Bioinfo]

I been Working in identification of Transposable Elements , Each class i had to choose different Tools and pipeline , when i saw you work here. Great work where i can have do all the analysis with one command in one platform, but to do it also required different operating system. sound challanging.

my task currently to identified a non ltr Elements in my Genome, while searching around found your scripts but seems will not work with my operating system and i have tried with MgeScan-nonLtr and i have failed as well, would you please assist me with a tool or one of the scripts you have build here to obtain nonLTR Results

[sestaton]

Hi, did you try the command above? You should be able to run the whole system and identify the elements you want without installing anything other than Docker.

If you are having trouble please let me know the output of the commands that cause errors.

[sestaton]

Any updates? I'd like to help if I can or close the issue of there's nothing to be done. Thanks.

[ohan-Bioinfo]

Still, having an issue , still couldn’t manage the ducker in my machine .
Will report the error soon
Please do not close it