Hoobari installation problem

[robertosirica]

Hello, I'm trying to install hoobari after downloading it as stated in the manual page but it gives me this error:

/usr/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'install_requires'
warnings.warn(msg)
running install
running build
running build_py
package init file 'src/init.py' not found (or not a regular file)
package init file 'src/init.py' not found (or not a regular file)
running build_ext
building 'phred' extension
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-J8eN0k/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -I/usr/include/python2.7 -c src/phred.c -o build/temp.linux-x86_64-2.7/src/phred.o
x86_64-linux-gnu-gcc: error: src/phred.c: File o directory non esistente
x86_64-linux-gnu-gcc: fatal error: no input files
compilation terminated.
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1

thank you

[tomwitz]

Hi, Hoobari requires python 3 and anaconda, and freebayes. I’ll add a more detailed installation guide. Regards, Tom

On Tue, 4 Jun 2019 at 16:15 robertosirica ***@***.***> wrote: Hello, I'm trying to install hoobari after downloading it as stated in the manual page but it gives me this error: /usr/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'install_requires' warnings.warn(msg) running install running build running build_py package init file 'src/*init*.py' not found (or not a regular file) package init file 'src/*init*.py' not found (or not a regular file) running build_ext building 'phred' extension x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-J8eN0k/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -I/usr/include/python2.7 -c src/phred.c -o build/temp.linux-x86_64-2.7/src/phred.o x86_64-linux-gnu-gcc: error: src/phred.c: File o directory non esistente x86_64-linux-gnu-gcc: fatal error: no input files compilation terminated. error: command 'x86_64-linux-gnu-gcc' failed with exit status 1 thank you — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#2?email_source=notifications&email_token=AESRJ2FSOUFCY7ODG6VFIDLPYZTFNA5CNFSM4HS4HKQKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4GXQ2L2A>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AESRJ2DMZRMSCTZEJTW4UM3PYZTFNANCNFSM4HS4HKQA> .

-- *Tom Rabinowitz* MD-PhD Student at Prof. Noam Shomron's Laboratory Sackler Faculty of Medicine, Room 303 *Tel-Aviv University* Tel-Aviv 6997801, Israel Tel: (972) 3640 7387 Fax: (972) 3640 7432

[robertosirica]

Thank you, I installed the softwares and added to PATH but the error remains,
am I doing something wrong?

[tomwitz]

1. What is the command that you run that returns this error?
2. If it's exactly the same message, it seems that your system still used python 2.7 to run hoobari. Try running hoobari using python3, e.g. python3 /path/to/hoobai

[robertosirica]

1. from hoobari folder:
   python3.7 ./setup.py build
2. I specified which python version to use.

thank you

[robertosirica]

It has no problems importing the libraries but it seems that the problem is in this line of the script where it searches for phred.c

phred = Extension('phred', sources=['src/phred.c'], libraries=['m'])

[tomwitz]

Oh, I'm sorry, we began writing a setup file when we used a c++ code to calculate the QUAL, but eventually we stayed with python only, and forgot to remove the setup file, which actually isn't required at all. Hoobari is a python tool which can be used right away after cloning, no installation is required. Thanks for raising the issue!

[robertosirica]

Ok, thank you again, so the right script to use in the fetal variant calling step is hoobari_main.py in src folder, is it right?

[tomwitz]

Exactly. I'm leaving this issue open until I add a short guide to README.