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@TobyBaril
TobyBaril committed May 6, 2024
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Expand Up @@ -169,13 +169,13 @@ If you would like to try Earl Grey, or prefer to use it in a browser, you can do

NOTE: This pipeline is currently running with Dfam 3.7 curated elements only. We are working on updating to Dfam 3.8 for a future release. If required, you can modify the conda installation of RepeatMasker within the conda environment (do at your own risk!)

Earl Grey version 4.2.3 (latest stable release) with all required and configured dependencies is found in the `toby_baril_bio` and `biooconda` conda channels. To install, simply run the following depending on your installation:
Earl Grey version 4.2.4 (latest stable release) with all required and configured dependencies is found in the `toby_baril_bio` and `biooconda` conda channels. To install, simply run the following depending on your installation:
```
# With conda
conda create -n earlgrey -c conda-forge -c bioconda earlgrey=4.2.3
conda create -n earlgrey -c conda-forge -c bioconda earlgrey=4.2.4
# With mamba
mamba create -n earlgrey -c conda-forge -c bioconda earlgrey=4.2.3
mamba create -n earlgrey -c conda-forge -c bioconda earlgrey=4.2.4
```

# Recommended Installation with Conda or Mamba on ARM-based Mac Systems (M chips)
Expand Down Expand Up @@ -349,7 +349,7 @@ brewIntel install coreutils

Change TEstrainer_for_earlGrey.sh for the macOS version:
```
nano $(which earlGrey | gsed 's|bin.*|share/earlgrey-4.2.3-0/scripts/TEstrainer/TEstrainer_for_earlGrey.sh|g')
nano $(which earlGrey | gsed 's|bin.*|share/earlgrey-4.2.4-0/scripts/TEstrainer/TEstrainer_for_earlGrey.sh|g')
# delete everything in this file.
```
Expand Down Expand Up @@ -555,12 +555,12 @@ Save the file with `CTRL+X` then press `Y` when asked to overwrite the file.

Make sure the updated file is executable:
```
chmod a+x $(which earlGrey | gsed 's|bin.*|share/earlgrey-4.2.3-0/scripts/TEstrainer/TEstrainer_for_earlGrey.sh|g')
chmod a+x $(which earlGrey | gsed 's|bin.*|share/earlgrey-4.2.4-0/scripts/TEstrainer/TEstrainer_for_earlGrey.sh|g')
```

Edit the script directory path in this file by running the following:
```
gsed -i "s|INSERT_FILENAME_HERE|$(which earlGrey | gsed 's:bin.*:share/earlgrey-4.2.3-0/scripts/TEstrainer/scripts/:g')|g" $(which earlGrey | gsed 's|bin.*|share/earlgrey-4.2.3-0/scripts/TEstrainer/TEstrainer_for_earlGrey.sh|g')
gsed -i "s|INSERT_FILENAME_HERE|$(which earlGrey | gsed 's:bin.*:share/earlgrey-4.2.4-0/scripts/TEstrainer/scripts/:g')|g" $(which earlGrey | gsed 's|bin.*|share/earlgrey-4.2.4-0/scripts/TEstrainer/TEstrainer_for_earlGrey.sh|g')
```

Edit famdb.py for use with our environment:
Expand All @@ -570,12 +570,12 @@ gsed -i 's/python3/python/g' $(which earlGrey | gsed 's|bin.*|share/RepeatMasker

Edit LTR_FINDER_PARALLEL to be compatible with zsh
```
gsed -i "s|\`timeout $timeout|\`gtimeout $timeout|g" $(which earlGrey | gsed 's|bin.*|share/earlgrey-4.2.3-0/scripts/LTR_FINDER_parallel|g')
gsed -i "s|\`timeout $timeout|\`gtimeout $timeout|g" $(which earlGrey | gsed 's|bin.*|share/earlgrey-4.2.4-0/scripts/LTR_FINDER_parallel|g')
```

Install LTR_Finder from source
```
cd $(which earlGrey | gsed 's|bin.*|share/earlgrey-4.2.3-0/scripts/bin|g')
cd $(which earlGrey | gsed 's|bin.*|share/earlgrey-4.2.4-0/scripts/bin|g')
git clone https://github.com/xzhub/LTR_Finder
cd ./LTR_Finder/source
make
Expand All @@ -584,14 +584,14 @@ cp * ../../LTR_FINDER.x86_64-1.0.7/

Edit rcMergeRepeatsLoose:
```
gsed -i 's|sed|gsed|g' $(which earlGrey | gsed 's|bin.*|share/earlgrey-4.2.3-0/scripts/rcMergeRepeatsLoose|g')
gsed -i 's|sed|gsed|g' $(which earlGrey | gsed 's|bin.*|share/earlgrey-4.2.4-0/scripts/rcMergeRepeatsLoose|g')
var=$(which earlGrey | gsed "s/earlGrey/Rscript/g")
gsed -i "s|Rscript|${var}|g" $(which earlGrey | gsed 's|bin.*|share/earlgrey-4.2.3-0/scripts/rcMergeRepeatsLoose|g')
gsed -i "s|Rscript|${var}|g" $(which earlGrey | gsed 's|bin.*|share/earlgrey-4.2.4-0/scripts/rcMergeRepeatsLoose|g')
```

Edit main earlGrey script:
```
gsed -i "s|Rscript|${var}|g" $(which earlGrey | gsed 's|bin.*|share/earlgrey-4.2.3-0/earlGrey|g')
gsed -i "s|Rscript|${var}|g" $(which earlGrey | gsed 's|bin.*|share/earlgrey-4.2.4-0/earlGrey|g')
```

Add an important directory to PERL5LIB (for RepeatMasker)
Expand All @@ -608,7 +608,7 @@ You are ready to go! Just remember to activate the _intel_ terminal, then the co
In this case, we need to bind a system directory to the docker container. In the line below, we are binding a directory call `host_data` that is found on our current path to `/data/` in the docker container. Please replace the file path before `:` to the directory you wish to bind to `/data/` in the container. This container must be run in interactive mode the first time you use it.

```
docker run -it -v `pwd`/host_data/:/data/ quay.io/biocontainers/earlgrey:4.2.3--h4ac6f70_0
docker run -it -v `pwd`/host_data/:/data/ quay.io/biocontainers/earlgrey:4.2.4--h4ac6f70_0
```

## If you are running the container for the first time, you need to enable Earl Grey to configure the Dfam libraries correctly in interactive mode.
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