fixes links

README.md

@@ -30,7 +30,7 @@ in this [GitHub repo](https://github.com/uab-cgds-worthey/DITTO-API).
 
 *Tools:*
 
-- Anaconda3 or pip3
+- Anaconda3
 - OpenCravat
 - Git
 
@@ -68,16 +68,16 @@ Please follow the steps mentioned in [install_openCravat.md](docs/install_openCr
 
 Create an environment via conda or pip. Below is an example to install `nextflow`.
 
-- [Python virtual environment](https://docs.python.org/3/tutorial/venv.html)
+- [Anaconda virtual environment](https://docs.anaconda.com/free/anaconda/install/index.html)
 
 ```sh
 # create environment. Needed only the first time. Please use the above link if you're not using Mac.
-python -m venv ditto-env
+conda create --name envi ditto-env
 
-source ditto-env/bin/activate
+conda activate ditto-env
 
-# Install nextflow and OpenCravat
-pip install nextflow
+# Install nextflow
+conda install bioconda::nextflow
 ```
 
 

docs/build_DITTO.md

@@ -1,6 +1,6 @@
 # DITTO
 
-:fire: DITTO (inspired by pokemon) is a tool for exploring any type of genetic variant and their predicted functional
+:fire: DITTO (inspired by pokemon) is a tool for exploring any type of small genetic variant and their predicted functional
 impact on transcript(s).
 
 :fire: DITTO uses an explainable neural network model to predict the functional impact of variants and utilizes SHAP to
@@ -20,8 +20,8 @@ sources.
 
 *Tools:*
 
-- Anaconda3 or pip3
-- OpenCravat
+- Anaconda3
+- OpenCravat-2.4.1
 - Git
 
 *Resources:*
@@ -63,7 +63,7 @@ conda activate training
 
 ### Setup OpenCravat (ignore if already installed)
 
-Please follow the steps mentioned in [install_openCravat.md](docs/install_openCravat.md).
+Please follow the steps mentioned in [install_openCravat.md](../docs/install_openCravat.md).
 
 ## Data
 
@@ -111,13 +111,13 @@ Follow the below steps to install and add more databases for annotation and befo
 
 2. Add the annotator to `mypackage/mypackage.yml` and reannotate the clinvar VCF file.
 
-3. Add the annotator to the [train config](configs/opencravat_train_config.json) and specify how to parse the
+3. Add the annotator to the [train config](../configs/opencravat_train_config.json) and specify how to parse the
    annotation.
 
 4. Follow the steps from Preprocessing above to parse, filter, process, tune and train DITTO.
 
 
 ## Benchmarking
 
-Please follow the [python notebook](src/analysis/opencravat_latest_benchmarking-Consequence_80_20.ipynb) to benchmark
+Please follow the [python notebook](../src/analysis/opencravat_latest_benchmarking-Consequence_80_20.ipynb) to benchmark
 DITTO with other pathogenicity predition tools. It also has code snippets to generate testing metrics and SHAP plots.

docs/install_openCravat.md

@@ -30,7 +30,7 @@ oc module install-base
 oc module  install aloft cadd cadd_exome cancer_genome_interpreter ccre_screen chasmplus civic clingen clinpred clinvar cosmic cosmic_gene cscape dann dann_coding dbscsnv dbsnp dgi ensembl_regulatory_build ess_gene exac_gene fathmm fathmm_xf_coding funseq2 genehancer gerp ghis gnomad gnomad3 gnomad_gene gtex gwas_catalog linsight loftool lrt mavedb metalr metasvm mutation_assessor mutationtaster mutpred1 mutpred_indel ncbigene ndex ndex_chd ndex_signor omim pangalodb phastcons phdsnpg phi phylop polyphen2 prec provean repeat revel rvis segway sift siphy spliceai uniprot vest cgc cgd varity_r
 ```
 
-Please look at the [install logs](docs/install_openCravat.logfile) for the versions of all the above annotators used to
+Please look at the [install logs](../docs/install_openCravat.logfile) for the versions of all the above annotators used to
 train the current DITTO model.
 
 ### Install reporter modules for DITTO