viromelab/tracespipe

Reconstruction and analysis of viral and host genomes at multi-organ level

tracespipe's Issues

Install

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

ERROR: trimmomatic is not installed.

I was following the installation instructions.

When I run

./TRACESPipe.sh --install

I get this error:

Downloading and Extracting Packages
mummer4-4.0.0rc1     | 636 KB    | #################################### | 100% 
Preparing transaction: done           
Verifying transaction: done
Executing transaction: done
Checking trimmomatic ... ERROR: trimmomatic is not installed.

But trimmomatic has been installed in the conda environment:

$ conda list | grep trim
trimmomatic               0.39                 hdfd78af_2    bioconda
$ conda run trimmomatic -version
0.39

What's wrong?

I'm using version d685d0c.

ERROR: ivar is not installed

Hello, despite running conda install ivar to install ivar, when I run the command ./TRACESPipe.sh --install, I get the following error:

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 ... SUCCESS! Checking mapDamage ... SUCCESS! Checking tabix ... SUCCESS! Checking AdapterRemoval ... SUCCESS! Checking bwa ... SUCCESS! Checking art_illumina ... SUCCESS! Checking blastn ... SUCCESS! Checking dnadiff ... SUCCESS! Checking ivar ... ERROR: ivar is not installed.

Do you have suggestions on how to navigate this error? Thank you so much!