03.-Installation-and-Execution.md

@@ -15,6 +15,15 @@ DIAMOND can take quite a bit of memory, and if you need to adjust the DIAMOND pa
 
 ## Installation
 
+
+### Conda installation
+The easiest and most reliable way to install SeqScreen is via `conda`. SeqScreen is hosted on [Bioconda](https://bioconda.github.io/user/install.html) and users can install the software as well as dependencies via 
+```
+conda install seqscreen
+```
+
+### Alternative installation methods
+#### Install from source
 The SeqScreen code can be installed and the most recent release checked out with the following command:
 ```
 git clone https://gitlab.com/treangenlab/seqscreen.git
@@ -36,7 +45,8 @@ mv ./nextflow ~/SOMEWHERE_IN_PATH
 
 In addition to Nextflow, users should also have Bash, Perl, Python 3, Java 8, Miniconda3, SciPy, and Jinja2 installed on their system, as described in the [SeqScreen Dependencies](https://gitlab.com/treangenlab/seqscreen/-/wikis/02.-SeqScreen-Dependencies) wiki page. 
 
-### Courtesy Installation Script
+
+#### Courtesy Installation Script
 We have compiled and packaged all of the software and database dependencies into an archive that can be downloaded and installed by running the `install/install_seqscreen.py` script in the SeqScreen repository. If, for example, you want to download and extract the required databases and software to `/path/to/requirements`, you would run
 ```
 python3 install/install_seqscreen.py --prefix /path/to/requirements -d -b
@@ -65,27 +75,23 @@ The SeqScreen pipeline can be run with multiple modes:
 
 The SeqScreen pipeline can be run in **default mode** with the following command:
 
-`nextflow run seqscreen.nf --fasta /Path/to/input.fasta --databases /Path/to/seqscreen_databases/ --working /Path/to/output_directory [--threads #] [--slurm]`
+`./seqscreen --fasta /Path/to/input.fasta --databases /Path/to/seqscreen_databases/ --working /Path/to/output_directory [--threads #] [--slurm]`
 
 For example, if you wanted to analyze one of the FASTA files in the example_data directory, you would run the following command:
 
-`nextflow run seqscreen.nf --fasta example_data/demo_sequences.fasta --databases /Path/to/seqscreen_databases/ --working ./output_directory --threads 30`
+`./seqscreen --fasta example_data/demo_sequences.fasta --databases /Path/to/seqscreen_databases/ --working ./output_directory --threads 30`
 
 In the following instance, you would run the SeqScreen pipeline and have it submit jobs to execution nodes on a SLURM-supported grid, where each CPU-intense job will request 30 cores per node:
 
-`nextflow run seqscreen.nf --fasta example_data/demo_sequences.fasta --databases /Path/to/seqscreen_databases/ --working ./output_directory --threads 30 --slurm`
-
-The SeqScreen pipeline can be run in the **batch mode** with the following command:
-
-`nextflow run seqscreen_batch.nf --fasta /Path/to/input.fasta --databases /Path/to/seqscreen_databases/ --working /Path/to/output_directory [--threads #] [--slurm]`
+`./seqscreen --fasta example_data/demo_sequences.fasta --databases /Path/to/seqscreen_databases/ --working ./output_directory --threads 30 --slurm`
 
 The SeqScreen pipeline can be run in the **fast mode** with the following command:
 
-`nextflow run seqscreen_fast.nf --fasta /Path/to/input.fasta --databases /Path/to/seqscreen_databases/ --working /Path/to/output_directory [--threads #] [--slurm]`
+`./seqscreen_fast --fasta /Path/to/input.fasta --databases /Path/to/seqscreen_databases/ --working /Path/to/output_directory [--threads #] [--slurm]`
 
 The following is an example of running SeqScreen default mode at the command line:
 
-`nextflow run seqscreen.nf --fasta example_data/demo_sequences.fasta --databases seqscreen_databases/ --working /pipelines/seqscreen_output --threads 20`
+`./seqscreen --fasta example_data/demo_sequences.fasta --databases seqscreen_databases/ --working /pipelines/seqscreen_output --threads 20`
 
 ```
 Output directory: ./seqscreen_output