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Author: fredjaya

pages/shelley-howto.md

@@ -43,7 +43,7 @@ shelley find bwa-mem2
 ![](assets/img/shelley_find_bwa-mem2.png)
 <br>
 </details>
-
+<br>
 
 **2.** Build a loadable module
 
@@ -56,6 +56,7 @@ shelley build bwa-mem2/2.3
 ![](assets/img/shelley_build_bwa-mem2.png)
 <br>
 </details>
+<br>
 
 **3.** Confirm the module was built succesfully
 
@@ -68,6 +69,7 @@ module avail
 ![](assets/img/module_avail.png)
 <br>
 </details>
+<br>
 
 **4.** Load the module
 
@@ -127,6 +129,7 @@ Shelley builds each tool in the file in sequence, showing a progress table as it
 ![](assets/img/shelley_build_tools-txt.png)
 <br>
 </details>
+<br>
 
 **3.** If a tool has more than one build for the same version (for example, several
 `--hash` builds of `samtools/1.21`), Shelley pauses and asks you to pick one.
@@ -136,6 +139,7 @@ Shelley builds each tool in the file in sequence, showing a progress table as it
 ![](assets/img/shelley_build_multiple-builds-prompt.png)
 <br>
 </details>
+<br>
 
 Use the arrow keys to select a build, then press Enter to continue the batch.
 
@@ -151,6 +155,7 @@ module avail
 ![](assets/img/shelley_build_tools-txt_summary.png)
 <br>
 </details>
+<br>
 
 ```
 ---------------------------------------------------------- /apps/Modules/modulefiles ----------------------------------------------------------
@@ -180,6 +185,7 @@ shelley find fastqc -v
 ![](assets/img/shelley_find_fastqc_v.png)
 <br>
 </details>
+<br>
 
 Each row corresponds to one `--hash` build of a version, with its buildable/installed
 status and the path you can copy into a config file, such as:
@@ -222,6 +228,7 @@ docker.io/library/busybox:1.34: removed 90 shared paths.
 ![](assets/img/shelley_build_bowtie2_unregistered.png)
 <br>
 </details>
+<br>
 
 If the version is missing from the upstream registry, Shelley creates a local registry
 entry from the CVMFS container itself and retries the install. This is transparent and
@@ -253,6 +260,7 @@ curation, all of these would be exposed by the module:
 ![](assets/img/shelley_build_vcftools_alias-select-all.png)
 <br>
 </details>
+<br>
 
 **2.** Type to filter the list down to the ones relevant to `vcftools`, for example `vcf`:
 
@@ -261,6 +269,7 @@ curation, all of these would be exposed by the module:
 ![](assets/img/shelley_build_vcftools_alias-filter-vcf.png)
 <br>
 </details>
+<br>
 
 **3.** Toggle each one you want with space, then press Enter once they're all selected:
 
@@ -269,6 +278,7 @@ curation, all of these would be exposed by the module:
 ![](assets/img/shelley_build_vcftools_alias-selected.png)
 <br>
 </details>
+<br>
 
 **4.** Shelley then asks whether to add or rename any aliases. Answer `n` to both to keep
 the selection as-is:
@@ -285,4 +295,5 @@ the selection as-is:
 ![](assets/img/shelley_build_vcftools_complete.png)
 <br>
 </details>
+<br>
 

pages/tools.md

@@ -91,6 +91,7 @@ You will see a list of available commands.
 ![](assets/img/shelley_help.png)
 <br>
 </details>
+<br>
 
 #### Finding a tool you already know by name
 
@@ -105,6 +106,7 @@ shelley find fastqc
 ![](assets/img/shelley_find_fastqc.png)
 <br>
 </details>
+<br>
 
 Shelley returns the tool's description together with its most recent container versions,
 plus whether it is installed as a module yet. `find` is forgiving about
@@ -129,6 +131,7 @@ Each result will show you the tool name and a brief description of what it does.
 ![](assets/img/shelley_search_de-novo-assembly.png)
 <br>
 </details>
+<br>
 
 {% include callout.html type="note" content="Search is under active development. All results are broad, and currently presented alphabetically. We recommend using shorter and more specific phrases as each extra word broadens the match rather than narrowing it, so a broad query like &quot;dna sequence quality control&quot; can return a large number of tools. Use the fewest, most specific terms you know, and remove words rather than adding them if you get too many results." %}
 
@@ -147,6 +150,7 @@ shelley find fastqc -v
 ![](assets/img/shelley_find_fastqc_v.png)
 <br>
 </details>
+<br>
 
 ### Building a module
 
@@ -163,6 +167,7 @@ This installs the most recent available version by default.
 ![](assets/img/shelley_build_fastqc.png)
 <br>
 </details>
+<br>
 
 {% include callout.html type="tip" content="To install a specific version instead of the most recent one, give `build` the same `<tool>/<version>` spec that `find -v` showed you, for example `shelley build fastqc/0.12.1`." %}