From cfef28d60599bf177f018bbf29cee05d264ad6fd Mon Sep 17 00:00:00 2001 From: Danilo Di Leo Date: Thu, 8 Feb 2024 13:57:04 +0100 Subject: [PATCH 1/8] add documentation for EUKulele bug --- docs/usage.md | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/docs/usage.md b/docs/usage.md index 95dde97b..25f52dd7 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -128,6 +128,31 @@ to the root directory of the EUKulele databases. > Please, check the [EUKulele documentation](https://eukulele.readthedocs.io/en/latest/#) for more information about the databases. +> There is a bug in EUKulele program that doesn't allow you to download some databases properly, check [EUKulele issue](https://github.com/AlexanderLabWHOI/EUKulele/issues/60). Meanwhile the developers are fixing this bug, we reccomand to download the database manually. To do so, follow these steps: + +- Create conda environment: +```bash +conda create -n EUKulele +conda activate EUKulele +conda install -c akrinos -c bioconda -c conda-forge EUKulele +``` + +- Download the database you need: +```bash +EUKulele download --database phylodb (you can use the name of the database you would like to download) +``` + +- Create the database tables: +```bash +cd eukulele/phylodb +mv reference.pep.fa reference.pep.fa.gz +gunzip reference.pep.fa.gz +create_protein_table.py --infile_peptide reference.pep.fa \ + --infile_taxonomy taxonomy-table.txt --outfile_json prot-map.json \ + --output tax-table.txt --delim "/" --col_source_id Source_ID \ + --taxonomy_col_id taxonomy --column SOURCE_ID +``` + From 24c721f86813a61e70a7fd907a974f2d414b33c5 Mon Sep 17 00:00:00 2001 From: Danilo Di Leo <78909156+danilodileo@users.noreply.github.com> Date: Thu, 8 Feb 2024 15:39:16 +0100 Subject: [PATCH 5/8] Update docs/usage.md Co-authored-by: Daniel Lundin --- docs/usage.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index d167d225..bd547e5b 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -133,9 +133,8 @@ to the root directory of the EUKulele databases. - Create conda environment: ```bash -conda create -n EUKulele +conda create -n -c akrinos -c bioconda -c conda-forge EUKulele EUKulele conda activate EUKulele -conda install -c akrinos -c bioconda -c conda-forge EUKulele ``` - Download the database you need: From 2d5b4b3f48b6d061724a02d22a0244950e099e81 Mon Sep 17 00:00:00 2001 From: Danilo Di Leo <78909156+danilodileo@users.noreply.github.com> Date: Thu, 8 Feb 2024 15:40:33 +0100 Subject: [PATCH 6/8] Update docs/usage.md Co-authored-by: Daniel Lundin --- docs/usage.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/usage.md b/docs/usage.md index bd547e5b..0506fa25 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -145,7 +145,7 @@ cd eukulele EUKulele download --database phylodb (you can use the name of the database you would like to download) ``` -- Create the database tables: +- Fix the problematic database tables: ```bash cd phylodb From 5cc6bf6f9f68d3b32dc765095d9f9e7e8d012e27 Mon Sep 17 00:00:00 2001 From: Danilo Di Leo <78909156+danilodileo@users.noreply.github.com> Date: Thu, 8 Feb 2024 15:41:15 +0100 Subject: [PATCH 7/8] Update usage.md --- docs/usage.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index 0506fa25..d3565515 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -142,13 +142,13 @@ conda activate EUKulele ```bash mkdir eukulele cd eukulele -EUKulele download --database phylodb (you can use the name of the database you would like to download) +EUKulele download --database mmetsp (you can use the name of the database you would like to download) ``` - Fix the problematic database tables: ```bash -cd phylodb +cd mmetsp mv reference.pep.fa reference.pep.fa.gz gunzip reference.pep.fa.gz create_protein_table.py --infile_peptide reference.pep.fa \ From f9afca42394fc876f7ae456fe0edcc029402ac9c Mon Sep 17 00:00:00 2001 From: Danilo Di Leo <78909156+danilodileo@users.noreply.github.com> Date: Thu, 8 Feb 2024 15:41:25 +0100 Subject: [PATCH 8/8] Update docs/usage.md Co-authored-by: Daniel Lundin --- docs/usage.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/usage.md b/docs/usage.md index d3565515..8358b04d 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -128,7 +128,7 @@ to the root directory of the EUKulele databases. > Please, check the [EUKulele documentation](https://eukulele.readthedocs.io/en/latest/#) for more information about the databases. -> :warning: There is a bug in EUKulele program that doesn't allow you to download some databases properly, check [EUKulele issue](https://github.com/AlexanderLabWHOI/EUKulele/issues/60). Meanwhile the developers are fixing this bug, we reccomand to download the database manually. To do so, follow these steps: +> :warning: There is currently a bug in the EUKulele program so that some databases properly do not download properly, check [EUKulele issue](https://github.com/AlexanderLabWHOI/EUKulele/issues/60). Until the developers have fixed this bug, we reccomend to download the database manually. To do so, follow these steps: - Create conda environment: