diff --git a/help/main/index.md b/help/main/index.md index b1ab249..e9d4c23 100644 --- a/help/main/index.md +++ b/help/main/index.md @@ -17,7 +17,7 @@ If you need an introduction to the terminology used in 'omics research or in anv {:.notice} -The help contents were last updated on **06 Sep 24 16:24:49** for anvi'o version **8-dev (marie)**. +The help contents were last updated on **09 Sep 24 10:20:12** for anvi'o version **8-dev (marie)**. {% include _project-anvio-version.html %} diff --git a/help/main/programs/anvi-draw-kegg-pathways/index.md b/help/main/programs/anvi-draw-kegg-pathways/index.md index 036fad3..af76eba 100644 --- a/help/main/programs/anvi-draw-kegg-pathways/index.md +++ b/help/main/programs/anvi-draw-kegg-pathways/index.md @@ -47,10 +47,10 @@ Write KEGG pathway map files incorporating data sourced from anvi'o databas ## Setup -There are hundreds of pathway maps, listed and categorized [here](https://www.genome.jp/kegg/pathway.html). [anvi-setup-kegg-data](/help/main/programs/anvi-setup-kegg-data) downloads the maps that have corresponding [files](https://www.kegg.jp/kegg/xml/) that allow elements of the map to be modified. Make sure to run that program with the `--kegg-snapshot` option to use the newest snapshot of [kegg-data](/help/main/artifacts/kegg-data), [`v2024-08-30`](https://figshare.com/articles/dataset/KEGG_build_2024-08-30/26880559?file=48903154), which includes pathway map files. +There are hundreds of pathway maps, listed and categorized [here](https://www.genome.jp/kegg/pathway.html). [anvi-setup-kegg-data](/help/main/programs/anvi-setup-kegg-data) downloads, among other files, the maps that have corresponding [XML files](https://www.kegg.jp/kegg/xml/) that allow elements of the map to be modified. The following command sets up the database in a default anvi'o directory.
-anvi-setup-kegg-data --kegg-snapshot v2024-08-30 +anvi-setup-kegg-data
Additional Python packages may be needed if you installed anvi'o `v8.0-dev` before this program's package requirements were included. These can be installed with the following command. @@ -61,7 +61,7 @@ pip install biopython ReportLab pymupdf frontend ### Download newest available files -Alternatively, KEGG data including maps can be set up not from a snapshot but by downloading the newest files available from KEGG using the `-D` flag. In the following command, a higher number of download threads than the default of 1 is provided by `-T`, which significantly speeds up downloading. +Alternatively, KEGG data can be set up not from a snapshot but by downloading the newest files available from KEGG using the `-D` flag. In the following command, a higher number of download threads than the default of 1 is provided by `-T`, which significantly speeds up downloading.
anvi-setup-kegg-data -D -T 5 @@ -69,10 +69,10 @@ anvi-setup-kegg-data -D -T 5 ### Install in non-default location -At the moment, KEGG data that includes maps does _not_ include "stray" KOs (see [anvi-setup-kegg-data](/help/main/programs/anvi-setup-kegg-data)) due to changes in the available model files. To preserve KEGG data that you already have set up, for this reason or another, the new snapshot or download can be placed in a non-default location using the option, `--kegg-data-dir`. +To preserve KEGG data that you already have set up for whatever reason, the new snapshot or download can be placed in a non-default location using the option, `--kegg-data-dir`.
-anvi-setup-kegg-data --kegg-snapshot v2024-08-30 --kegg-data-dir path/to/other/directory +anvi-setup-kegg-data --kegg-data-dir path/to/other/directory
`anvi-draw-kegg-pathways` requires a `--kegg-dir` argument to seek KEGG data in a non-default location. diff --git a/help/main/programs/anvi-reaction-network/index.md b/help/main/programs/anvi-reaction-network/index.md index f54c4c6..8234f9e 100644 --- a/help/main/programs/anvi-reaction-network/index.md +++ b/help/main/programs/anvi-reaction-network/index.md @@ -51,10 +51,10 @@ Information on the predicted reactions and the involved metabolites are stored i ## Setup -[anvi-setup-kegg-data](/help/main/programs/anvi-setup-kegg-data) downloads [binary relations files](https://www.genome.jp/brite/br08906) needed to construct a [reaction-network](/help/main/artifacts/reaction-network) from [KEGG Orthology (KO)](https://www.genome.jp/kegg/ko.html) sequence annotations. Make sure to run that program with the `--kegg-snapshot` option to use the newest snapshot of [kegg-data](/help/main/artifacts/kegg-data), [`v2024-08-30`](https://figshare.com/articles/dataset/KEGG_build_2024-08-30/26880559?file=48903154), which includes binary relations files. +[anvi-setup-kegg-data](/help/main/programs/anvi-setup-kegg-data) downloads, among other files, the [binary relations files](https://www.genome.jp/brite/br08906) needed to construct a [reaction-network](/help/main/artifacts/reaction-network) from [KEGG Orthology (KO)](https://www.genome.jp/kegg/ko.html) sequence annotations. The following command sets up the database in a default anvi'o directory.
-anvi-setup-kegg-data --kegg-snapshot v2024-08-30 +anvi-setup-kegg-data
[anvi-setup-modelseed-database](/help/main/programs/anvi-setup-modelseed-database) sets up the [ModelSEED Biochemistry database](https://github.com/ModelSEED/ModelSEEDDatabase), which harmonizes biochemical data from various reference databases, including KEGG. The following command sets up the database in a default anvi'o directory. @@ -65,7 +65,7 @@ anvi-setup-modelseed-database ### Download newest available KEGG files -Alternatively, KEGG data including binary relations files can be set up not from a snapshot but by downloading the newest files available from KEGG using the `-D` flag. In the following command, a higher number of download threads than the default of 1 is provided by `-T`, which significantly speeds up downloading. +Alternatively, KEGG data can be set up not from a snapshot but by downloading the newest files available from KEGG using the `-D` flag. In the following command, a higher number of download threads than the default of 1 is provided by `-T`, which significantly speeds up downloading.
anvi-setup-kegg-data -D -T 5 @@ -73,16 +73,20 @@ anvi-setup-kegg-data -D -T 5 ### Install in non-default location -At the moment, KEGG data that includes binary relations files does _not_ include "stray" KOs (see [anvi-setup-kegg-data](/help/main/programs/anvi-setup-kegg-data)) due to changes in the available model files. To preserve KEGG data that you already have set up, for this reason or another, the new snapshot or download can be placed in a non-default location using the option, `--kegg-data-dir`. +To preserve KEGG data that you already have set up for whatever reason, the new snapshot or download can be placed in a non-default location using the option, `--kegg-data-dir`.
-anvi-setup-kegg-data --kegg-snapshot v2024-08-30 --kegg-data-dir path/to/other/directory +anvi-setup-kegg-data --kegg-data-dir path/to/other/directory
`anvi-reaction-network` requires a `--kegg-dir` argument to seek KEGG data in a non-default location. Likewise, different versions of the ModelSEED Biochemistry database can be set up in non-default locations and used with the `--modelseed-dir` argument. +
+anvi-setup-modelseed-database --dir path/to/other/directory +
+ ## Usage [anvi-reaction-network](/help/main/programs/anvi-reaction-network) takes a either a [contigs-db](/help/main/artifacts/contigs-db) OR a [pan-db](/help/main/artifacts/pan-db) and [genomes-storage-db](/help/main/artifacts/genomes-storage-db) as required input. Genes stored within the [contigs-db](/help/main/artifacts/contigs-db) or [genomes-storage-db](/help/main/artifacts/genomes-storage-db) must have KO protein annotations, which can be assigned by [anvi-run-kegg-kofams](/help/main/programs/anvi-run-kegg-kofams).