latest version no configure file

[dcm9123]

Hi, I was trying to install the latest version where you guys debugged the 'prop' error (which is what I was getting before with earlier versions). However, after I download the tar ball of the new release, I can't see a config file like the other tarballs. After realizing this I ran autoconf, and then it generated the configure file. When I ran the command posted in your readme.md, ./configure --prefix=/usr/local/shorah/ PYTHON=/usr/local/shorah/bin/python3.6 it gave me the following output:

checking whether configure should try to set CXXFLAGS/CPPFLAGS/LDFLAGS... yes
./configure: line 1860: AX_CHECK_ENABLE_DEBUG: command not found
configure: error: cannot find install-sh, install.sh, or shtool in "." "./.." "./../.."

I am relatively new to programming, so I am kind of lost here... I am not sure where to find the install.sh to keep going. Thanks in advance,

[DrYak]

Thank you for pointing out the missing bootstraping. I have updated the files accordingly.

For the record, the necessary sequence to bootstrap is:

aclocal -I m4
autoconf
automake -a -c

It requires a version of automake of at least 1.15.0 (it might be missing on some older cluster installations relying on older LTS version of distributions).

Could you please give a try again with the updated .tar.bz2 / .tar.xz ? (or with the above sequence if you want to do it manually) Thank you very much.

[dcm9123]

Hi, It is working now. The executables are in the virtual environment I created. I will be running my data to see if it works fine now. Thanks a lot!

[dcm9123]

Hi again,

So I tried running my data in my virtual environment /usr/local/shorah/bin , and whenever I try the following command:

sudo ./shorah shotgun -b sample1_sorted.bam -f msp1.fasta

I get the following output from it:

Executable fil not found, compile first.

This also happens when I run sudo ./shorah amplicon. However, when I run just sudo ./shorah , I get this, as if it was properly compiled and working:

usage: shorah <subcommand> [options]

optional arguments:
  -h, --help            show this help message and exit
  -v, --version         show program's version number and exit

sub-commands:
  {shotgun,amplicon,snv}
                        available sub-commands
    shotgun             run local analysis in shotgun mode
    amplicon            run local analysis in amplicon mode
    snv                 run single-nucleotide-variant calling

Run shorah subcommand -h for more help

[DrYak]

Two different things:

Privileges

running shorah does not require any root privileges. You do not need to use sudo to run it.

Paths

The fact that you need to explicitely specify ./ makes me think you probably don't have /usr/local/shorah/bin in your path (echo $PATH to check).

You can add this directory to the path by typing export PATH="/usr/local/shorah/bin:${PATH}". This will add it to the path where executables are searched for.

• Thus you can then only type shorah to run it.
• Shorah in turn will be able to find its submodules (such as fil, b2w and diri_sampler).

The same is also needed for the python module. If you get errors about python modules not being found, it means your need to set a PYTHONPATH. You need to type export PYTHONPATH="/usr/local/shorah/lib/python{ver}/site-packages where {ver} == the version of python that you used. e.g.: export PYTHONPATH="/usr/local/shorah/lib/python3.7/site-packages (Just check the content of the directory: ls /usr/local/shorah/lib/ or use the [TAB] key on your keybaord to auto-complete.).

[dcm9123]

Yes! This fixed it! Thanks a lot for the insight, now my data is running fine.