From 11556e7d31640917f11d91957348a47b1121fa9f Mon Sep 17 00:00:00 2001
From: dariober <dario.beraldi@gmail.com>
Date: Mon, 16 Dec 2024 13:49:12 +0000
Subject: [PATCH] Edit how to add evidence tracks jbrowse; Edit header
MIME-Version: 1.0
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Do not cd to `jbrowse_data` otherwise you get:

```
apollo jbrowse get-config
    Error: Configuration file "/root/.config/apollo-cli/config.yml" does not
    exist. Please run "apollo config" first
```

Write config.json to `data/` so docker can see it otherwise you get:

```
apollo jbrowse set-config config.json
 ›   Error: File config.json does not exist
```

---

Docs header merged to be more consistent with text.
---
 .../try-it-out/02-loading-data.md             | 20 +++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/packages/website/docs/getting-started/try-it-out/02-loading-data.md b/packages/website/docs/getting-started/try-it-out/02-loading-data.md
index 00213241..e03361a7 100644
--- a/packages/website/docs/getting-started/try-it-out/02-loading-data.md
+++ b/packages/website/docs/getting-started/try-it-out/02-loading-data.md
@@ -66,7 +66,7 @@ apollo login
 If you need to log in again, run `apollo logout` first, or use
 `apollo login --force`.
 
-## Adding assemblies
+## Adding assemblies and annotations
 
 The next step is to add an assembly. We're going to use use trimmed-down
 assembly that only includes a single chromosome. This is so that the data is
@@ -96,8 +96,6 @@ apollo feature \
   --assembly 'Schistosoma mansoni'
 ```
 
-## Adding annotations
-
 Next we're going to add a second assembly and set of annotations. This assembly
 is from the related species Schistosoma haematobium. Run these two commands to
 add the assembly and annotations:
@@ -149,8 +147,7 @@ The first step is to get the JBrowse configuration stored in Apollo so we can
 update it. Run these commands:
 
 ```sh
-cd jbrowse_data/
-apollo jbrowse get-config >config.json
+apollo jbrowse get-config > data/config.json
 ```
 
 Now that we have the configuration, we can use the `jbrowse` CLI tool to add the
@@ -163,22 +160,25 @@ jbrowse add-track \
   data/smansoni_SM_v10_3_subset.cram \
   --load inPlace \
   --name "S. mansoni RNA-seq" \
-  --assemblyNames "${MANSONI_ID}"
+  --assemblyNames "${MANSONI_ID}" \
+  --out data/config.json
 jbrowse add-track \
   data/shaematobium_CHR_3_subset.cram \
   --load inPlace \
   --name "S. haematobium RNA-seq" \
-  --assemblyNames "${HAEMATOBIUM_ID}"
+  --assemblyNames "${HAEMATOBIUM_ID}" \
+  --out data/config.json
 jbrowse add-track \
   data/shaematobium_vs_smansoni.paf \
   --load inPlace \
   --name "S. haematobium vs. S. mansoni TBLASTX" \
-  --assemblyNames "${HAEMATOBIUM_ID}","${MANSONI_ID}"
+  --assemblyNames "${HAEMATOBIUM_ID}","${MANSONI_ID}" \
+  --out data/config.json
 ```
 
 Now the last step is to send the updated JBrowse config back to Apollo.
 
 ```sh
-apollo jbrowse set-config config.json
-rm config.json
+apollo jbrowse set-config data/config.json
+rm data/config.json
 ```