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Edit how to add evidence tracks jbrowse; Edit header
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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.
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dariober committed Dec 16, 2024
1 parent 5bc954a commit 11556e7
Showing 1 changed file with 10 additions and 10 deletions.
20 changes: 10 additions & 10 deletions packages/website/docs/getting-started/try-it-out/02-loading-data.md
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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:
Expand Down Expand Up @@ -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
Expand All @@ -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
```

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