update BRAKER (#43)

* update BRAKER * Update BRAKER.md Signed-off-by: Cal <[email protected]> --------- Signed-off-by: Cal <[email protected]> Co-authored-by: Cal <[email protected]>
nesi · Dec 5, 2023 · b0c377e · b0c377e
1 parent fd4f502
commit b0c377e
Showing 1 changed file with 10 additions and 27 deletions.
diff --git a/docs/Scientific_Computing/Supported_Applications/BRAKER.md b/docs/Scientific_Computing/Supported_Applications/BRAKER.md
@@ -3,22 +3,12 @@ created_at: '2023-03-06T19:04:56Z'
 hidden: false
 position: 0
 tags: []
-title: BRAKER
 vote_count: 0
 vote_sum: 0
 zendesk_article_id: 6529511928207
 zendesk_section_id: 360000040076
 ---
 
-
-
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-!!! warning
-    This page has been automatically migrated and may contain formatting errors.
-[//]: <> (^^^^^^^^^^^^^^^^^^^^)
-[//]: <> (REMOVE ME IF PAGE VALIDATED)
-
 ## Description
 
 The rapidly growing number of sequenced genomes requires fully automated
@@ -67,29 +57,22 @@ Artistic License
 ## Prerequisites
 
 
-!!! prerequisite Obtain GeneMark-ES/ET Academic License 
-     GeneMark-ES/ET which is one of the dependencies for BRAKER requires an
-     individual academic license  (this is free). This can be obtained as
-     below
-     -   Download URL
-         <http://topaz.gatech.edu/genemark/license_download.cgi>
-
-
+!!! prerequisite "Obtain GeneMark-ES/ET Academic License"
+
+    GeneMark-ES/ET which is one of the dependencies for BRAKER requires an individual academic license  (this is free). This can be obtained as below
+     -   Download URL <http://topaz.gatech.edu/genemark/license_download.cgi>
      -   ![genemark\_es\_license.png](../../assets/images/BRAKER.png)
      -   Downloaded filename will be in the format of **gm\_key\_64.gz. **
      -   Decompress this file with `gunzip gm_key_64.gz`  and move it to
-         home directory as  a **hidden** file under the filename `.gm_key`
-          .i.e. `~/.gm_key`
+         home directory as  a **hidden** file under the filename `.gm_key` .i.e. `~/.gm_key`
 
-!!! prerequisite Copy AUGUSTUS config to a path with read/write permissions
-     Make a copy of AUGUSTUS config from
-     ***/opt/nesi/CS400\_centos7\_bdw/AUGUSTUS/3.4.0-gimkl-2022a/config***
-      to path with read/write permissions .i.e. project, nobackup,home 
+!!! info "Copy AUGUSTUS config to a path with read/write permissions"
+
+    Make a copy of AUGUSTUS config from ***/opt/nesi/CS400\_centos7\_bdw/AUGUSTUS/3.4.0-gimkl-2022a/config*** to path with read/write permissions .i.e. project, nobackup,home 
 
 ### Example Slurm scripts
 
-Following example uses the .fa files provided BRAKER developers on
-<https://github.com/Gaius-Augustus/BRAKER/tree/master/example>
+Following example uses the [.fa files provided BRAKER developers](https://github.com/Gaius-Augustus/BRAKER/tree/master/example)
 
 ``` sl
 #!/bin/bash -e
@@ -123,4 +106,4 @@ augustus.hints_iter1.aa        errors/      hintsfile.gff          uniqueSeeds.g
 augustus.hints_iter1.codingseq evidence.gff hintsfile_iter1.gff    what-to-cite.txt
 augustus.hints_iter1.gff       GeneMark-EP/ prevHints.gff 
 augustus.hints_iter1.gtf       GeneMark-ES/ proteins.fa 
-```
+```