Install

[Turstein]

In the installation instructions, there is no information indicating that dependent software must be installed manually.

I have started installing trimmomatic, cryfa and so on manually with conda, which is OK, but not so great when I suspect there is something wrong with the --install function? Could you provide version information for dependent software?

Progress so far:

:~/traces/tracespipe/src$ ./TRACESPipe.sh --install

Checking trimmomatic ... SUCCESS!
Checking cryfa ... SUCCESS!
Checking MAGNET ... SUCCESS!
Checking FALCON ... SUCCESS!
Checking gto ... SUCCESS!
Checking spades.py ... SUCCESS!
Checking igv ... SUCCESS!
Checking bowtie2 ... SUCCESS!
Checking samtools ... SUCCESS!
Checking bcftools ... SUCCESS!
Checking bedops ... SUCCESS!
Checking bedtools ... SUCCESS!
Checking fastq_pair ... SUCCESS!
Checking efetch ... ERROR: efetch is not installed.
TIP: Try: ./TRACESPipe.sh --install

Installation instructions

To install TRACESPipe, run the following commands in a Linux OS:

git clone https://github.com/viromelab/tracespipe.git
cd tracespipe/src/
chmod +x TRACES*.sh
./TRACESPipe.sh --install
./TRACESPipe.sh --get-all-aux

[mirakaya]

Thank you for your interest in TRACESPipe.

Conda has been updated since then and there are many conflicts. Some of the tools, such as efetch may have to be installed without conda. For example, efetch can be installed using

sudo apt install ncbi-entrez-direct -y

Nevertheless, we have changed the code to allow all tools to be verified without breaking the verification if some tool has not been installed.

Kind regards,
Maria

[zacherydickson]

I also had a similar problem with the --install function.

From what I can see it looks like the CHECK_PROGRAMS function is called (line 1073) before checking if the --install switch was specified (line 1317).
As a result the TRACESPipe.sh script fails to call the TRACES_install.sh script if the latter hasn't been manually run already.

I recommend reordering some of the if blocks, or only checking dependencies in cases where the dependencies will be required.

~Zach