Training vids and PDFs (#96)

* Add training videos and powerpoints

* Update readme with information about Git LFS

* Update Gemfile.lock dependencies

* Add arrays and nanopore PDFs

* Restore Gemfile

* Update to Ruby 2.7 on Travis

Author: morgantaschuk

.gitattributes

@@ -0,0 +1,2 @@
+presentations/miso_intro.mp4 filter=lfs diff=lfs merge=lfs -text
+presentations/miso_samples.mp4 filter=lfs diff=lfs merge=lfs -text

.travis.yml

@@ -2,7 +2,7 @@ language: ruby
 git:
   depth: 3
 rvm:
-  - 2.3
+  - 2.7
 cache: bundler
 script:
   - bundle exec jekyll build

0-0-0-introduction.md

@@ -0,0 +1,17 @@
+---
+layout: page
+category: walkthrough
+title: Introduction to MISO
+is-detailed: true
+
+---
+
+
+<video muted autoplay controls>
+    <source src="presentations/miso_intro.mp4" type="video/mp4">
+</video>
+
+[Download the PDF]({{ '/presentations/intro.pdf' | prepend: site.baseurl }})
+
+
+<a href="index">Home</a> | <a href="0-0-admin-tasks">Administration Tasks</a> >

0-0-admin-tasks.md

@@ -33,7 +33,7 @@ Active Directory group.
 OICR uses Active Directory authentication for MISO. Users must be added by IT; once added,
 they can then log in to MISO using their email credentials.
 
-1. Please email [email protected] and CC Morgan Taschuk to request that the user be added to MISO LIMS by 
+1. Please email [email protected] and CC Morgan Taschuk to request that the user be added to MISO LIMS by
 making them part of the following Active Directory groups:
     * If the person is to be added as an admin: `MISO_ROLE_ADMIN` and `MISO_ROLE_INTERNAL` groups.
     * If the person is not to be given admin access: `MISO_ROLE_INTERNAL` group.
@@ -43,4 +43,4 @@ making them part of the following Active Directory groups:
 {% include admin-reports.md %}
 
 
-<a href="index">Home</a> | <a href="1-0-project-coordination">Project Coordination tutorial</a> > 
+< <a href="0-0-0-introduction">Introduction to MISO</a> | <a href="index">Home</a> | <a href="1-0-project-coordination">Project Coordination tutorial</a> > 

2-0-samples.md

@@ -8,6 +8,14 @@ section: 3.4
 
 ---
 
+<video muted autoplay controls>
+    <source src="presentations/miso_samples.mp4" type="video/mp4">
+</video>
+
+[Download the PDF]({{ '/presentations/samples.pdf' | prepend: site.baseurl }})
+
+
+
 <div id="toc">
 Table of Contents
 <ol>
@@ -63,21 +71,21 @@ the Project you created in the last session.
 
 ## 2.1 Entering a Tissue
 
-All samples in MISO are entered using the bulk entry screen. We will start by 
+All samples in MISO are entered using the bulk entry screen. We will start by
 entering a single Sample for reference tissue from the Identity `ID1`.
 
 {% include samples-receiving.md detailed=page.is-detailed quantity=page.quantity %}
-    1. _External Name_: this is the name of the *individual donor*, whether internal or 
-       external. For example, an external name would be "Morgan" (internally we refer to 
+    1. _External Name_: this is the name of the *individual donor*, whether internal or
+       external. For example, an external name would be "Morgan" (internally we refer to
        her as plain ol' MORG_0001).
         * Enter `PROJ_ID1` in the _External Name_ field, replacing `PROJ` with your project's
-          short name. Record this in your worksheet.  <img src="pics/blue_pencil.png"> 
-            * Once you enter an external name, MISO will go and find any existing donors with 
-              external name(s) that match this, and will add them to the dropdown menu for the 
+          short name. Record this in your worksheet.  <img src="pics/blue_pencil.png">
+            * Once you enter an external name, MISO will go and find any existing donors with
+              external name(s) that match this, and will add them to the dropdown menu for the
               _Identity Alias_ field.
-            * If there are no existing donors with the exact external name, the option of 
-              `First Receipt (project short name)` will be available. 
-            * If more than one option is available in the _Identity Alias_ dropdown, the cell 
+            * If there are no existing donors with the exact external name, the option of
+              `First Receipt (project short name)` will be available.
+            * If more than one option is available in the _Identity Alias_ dropdown, the cell
               will be displayed with a light purple background.
     1. Select `First Receipt (project short name)` for the _Identity Alias_.
     1. _Donor Sex_: Select any item from the dropdown.
@@ -100,7 +108,7 @@ lines. For more information about Sample nomenclature, see <a
 href="https://wiki.oicr.on.ca/display/GENOMICS/LIMS+Guidelines#LIMSGuidelines-SampleNomenclature"
 target="_new">Sample Nomenclature</a> on the GENOMICS wiki.
 
-Record the alias in your worksheet. <img src="pics/blue_pencil.png"> 
+Record the alias in your worksheet. <img src="pics/blue_pencil.png">
 
 ## 2.2 Automatically created Samples
 
@@ -174,12 +182,12 @@ cell. You can also click and drag to only fill in a certain number of cells.
 1. Fill in the columns in the same way for: _Sample Type_, _Project_, _Donor Sex_,
    _Tissue Origin_, _Tissue Type_, _Times Received_, _Tube Number_, _Material_, and
    _QC Status_.
-1. _Description_: Copying and pasting from Excel and Word is supported. 
+1. _Description_: Copying and pasting from Excel and Word is supported.
    Copy something from anywhere and press Ctrl+V (Windows & Linux) or Command+V (Mac)
    on your keyboard to paste.
 
-1. _Matrix Barcode_: you would normally use a hand-scanner or copy and paste a list of 
-barcodes from a spreadsheet. For each sample, select a barcode, scan or type it in, and record 
+1. _Matrix Barcode_: you would normally use a hand-scanner or copy and paste a list of
+barcodes from a spreadsheet. For each sample, select a barcode, scan or type it in, and record
 it in your worksheet. <img src="pics/blue_pencil.png">
 1. _External Name_:  Again, this is the name of the *individual*, whether internal or external.
 Here's a suggested list. Replace `PROJ` with your own project short name.
@@ -190,18 +198,18 @@ Here's a suggested list. Replace `PROJ` with your own project short name.
   1. Because you've already created an Identity with the external name `PROJ_ID1`, it is found as a match
 to the external name you entered for the top row. In the `Identity Alias` dropdown menu for the first row,
 select the existing Identity.
-  1. Select `First Receipt` from the dropdown menu in each remaining cell of the `Identity Alias` column. 
+  1. Select `First Receipt` from the dropdown menu in each remaining cell of the `Identity Alias` column.
 
 Some fields cannot be filled down, so enter each of those separately. If you
-have a label with an incrementing number (_e.g._, `1`, `2`), enter two rows, select them, 
+have a label with an incrementing number (_e.g._, `1`, `2`), enter two rows, select them,
 then double click the blue square.
 
 1. _Secondary ID_: enter `BioBankID 2` in the second row. Select the _Secondary Identifier_
 fields for rows 1 and 2, then double click the blue square to fill down rows 3 and 4.
 1. Click _Save_ at the upper right hand corner.
 
 If everything is correct, the _Sample Alias_ and _Sample Name_ will be auto-generated for each row and
-the samples will be saved. 
+the samples will be saved.
 Record the external name, sample class, alias, and barcode in your worksheet. <img src="pics/blue_pencil.png">
 If you navigate back to your _Edit Project_ page, there should be nine Samples:
 
@@ -236,7 +244,7 @@ material of an existing Identity.
   * _Project_: Select your project.
   * _Scientific Name_: `Homo sapiens`.
   * _External Name_: `PROJ_ID2` (where `PROJ` is your project's short name) .
-  * _Identity Alias_: The existing identity should be selected automatically 
+  * _Identity Alias_: The existing identity should be selected automatically
     in the dropdown menu.
   * _Tissue Origin_: `nn (Unknown)`
   * _Tissue Type_: `R (Reference or non-tumour, non-diseased tissue sample)`
@@ -273,7 +281,7 @@ hidden from the MISO interface.
 # 2.5 Scanning tissues and stocks into a Box
 
 In this section we will add the stocks and tissues you just received into your
-inbox for further work. 
+inbox for further work.
 
 {% include inboxes.md %}
 
@@ -369,8 +377,8 @@ items.".
 Propagate again from the 4 _gDNA (stock)_ samples to _gDNA (aliquot)_.
 
 1. If you are continuing from the end of section **3.3 Bulk Editing**, do not
-  navigate away from the page. 
-    1. At the top left of the table after saving samples, click the _Propagate_ button. 
+  navigate away from the page.
+    1. At the top left of the table after saving samples, click the _Propagate_ button.
     1. Enter _1_ for the number of replicates (child samples to be created from each parent)
     and _gDNA (aliquot)_ for the type of child sample. Continue to step 3.
 1. Otherwise, select samples using the following:

3-0-libraries.md

@@ -6,6 +6,9 @@ is-detailed: true
 
 ---
 
+<object data="presentations/libraries.pdf" width="800" height="500" type='application/pdf'> </object>
+
+
 <div id="toc">
 Table of Contents
 <ol>
@@ -66,19 +69,19 @@ and indices can be added based on the box position.
 1. On the _Boxes_ page, find your box and click on its link.
 1. Select all the aliquots in your box by control-clicking all the aliquots
 in the box (command-click on a Mac). If the aliquots are all in one row or column,
-you can click on the row/column header to select all items in that row or column. 
+you can click on the row/column header to select all items in that row or column.
 Use control-click (or command-click) to select more than one row or column.
-1. Click the _Propagate_ button at the top left of the box contents table. If the 
+1. Click the _Propagate_ button at the top left of the box contents table. If the
 top left of the box contents table indicates that more than one type of element is
 selected, de-select the non-aliquot tubes and then click _Propagate_.
 1. Choose _1_ replicate.
 1. Click _Propagate_.
 1. From the bulk libraries table, you can now sort the libraries you are creating
-based on their parent sample's position within the box. Sorting can be done by 
+based on their parent sample's position within the box. Sorting can be done by
 rows (`A01`, `A02`, `B01`, `B02`, ...) or columns (`A01`, `B01`, `A02`, `B02`, ...).
-  * This may be useful when using the Sciclone robot to create libraries and add 
+  * This may be useful when using the Sciclone robot to create libraries and add
 indices at a particular plate location. Once the libraries are sorted based on the
-parent sample's location, the indices can be copy-pasted in the order that the 
+parent sample's location, the indices can be copy-pasted in the order that the
 robot requires.
 
 {% include libraries-receipt.md detailed=page.is-detailed section=3
@@ -114,4 +117,3 @@ to get assistance from the MISO team.
 
 
 < <a href="2-0-samples">Samples tutorial</a> | <a href="index">Home</a> | <a href="4-0-sequencing">Sequencing tutorial</a> >
-

4-0-sequencing.md

@@ -6,6 +6,9 @@ is-detailed: true
 
 ---
 
+<object data="presentations/sequencing.pdf" width="800" height="500" type='application/pdf'> </object>
+
+
 <div id="toc">
 Table of Contents
 <ol>

5-0-arrays.md

@@ -6,6 +6,9 @@ is-detailed: true
 
 ---
 
+<object data="presentations/miso_array_training.pdf" width="800" height="500" type='application/pdf'> </object>
+
+
 <div id="toc">
 Table of Contents
 <ol>
@@ -30,4 +33,3 @@ Table of Contents
 {% include array_runs.md detailed=page.is-detailed %}
 
 < <a href="index">Home</a> >
-

6-0-oxford-nanopore.md

@@ -6,6 +6,9 @@ is-detailed: true
 
 ---
 
+<object data="presentations/miso_ont_training.pdf" width="800" height="500" type='application/pdf'> </object>
+
+
 <div id="toc">
 Table of Contents
 <ol>
@@ -34,4 +37,3 @@ Table of Contents
 {% include ont_runs_add_pools.md %}
 
 < <a href="index">Home</a> >
-

Gemfile

@@ -3,4 +3,3 @@ gem 'github-pages', group: :jekyll_plugins
 gem "minima"
 gem 'therubyracer'
 gem "rake"
-

Gemfile.lock

@@ -1,7 +1,7 @@
 GEM
   remote: https://rubygems.org/
   specs:
-    activesupport (4.2.9)
+    activesupport (4.2.10)
       i18n (~> 0.7)
       minitest (~> 5.1)
       thread_safe (~> 0.3, >= 0.3.4)
@@ -13,24 +13,25 @@ GEM
       execjs
     coffee-script-source (1.11.1)
     colorator (1.1.0)
-    commonmarker (0.17.9)
+    commonmarker (0.17.13)
       ruby-enum (~> 0.5)
     concurrent-ruby (1.0.5)
-    dnsruby (1.60.2)
+    dnsruby (1.61.3)
+      addressable (~> 2.5)
     em-websocket (0.5.1)
       eventmachine (>= 0.12.9)
       http_parser.rb (~> 0.6.0)
-    ethon (0.11.0)
+    ethon (0.12.0)
       ffi (>= 1.3.0)
     eventmachine (1.2.7)
     execjs (2.7.0)
-    faraday (0.15.2)
+    faraday (1.0.1)
       multipart-post (>= 1.2, < 3)
     ffi (1.9.23)
     forwardable-extended (2.6.0)
-    gemoji (3.0.0)
-    github-pages (185)
-      activesupport (= 4.2.9)
+    gemoji (3.0.1)
+    github-pages (186)
+      activesupport (= 4.2.10)
       github-pages-health-check (= 1.8.1)
       jekyll (= 3.7.3)
       jekyll-avatar (= 0.5.0)
@@ -71,7 +72,7 @@ GEM
       listen (= 3.1.5)
       mercenary (~> 0.3)
       minima (= 2.4.1)
-      nokogiri (>= 1.8.1, < 2.0)
+      nokogiri (>= 1.8.2, < 2.0)
       rouge (= 2.2.1)
       terminal-table (~> 1.4)
     github-pages-health-check (1.8.1)
@@ -80,7 +81,7 @@ GEM
       octokit (~> 4.0)
       public_suffix (~> 2.0)
       typhoeus (~> 1.3)
-    html-pipeline (2.8.0)
+    html-pipeline (2.13.0)
       activesupport (>= 2)
       nokogiri (>= 1.4)
     http_parser.rb (0.6.0)
@@ -104,9 +105,9 @@ GEM
     jekyll-coffeescript (1.1.1)
       coffee-script (~> 2.2)
       coffee-script-source (~> 1.11.1)
-    jekyll-commonmark (1.2.0)
+    jekyll-commonmark (1.3.1)
       commonmarker (~> 0.14)
-      jekyll (>= 3.0, < 4.0)
+      jekyll (>= 3.7, < 5.0)
     jekyll-commonmark-ghpages (0.1.5)
       commonmarker (~> 0.17.6)
       jekyll-commonmark (~> 1)
@@ -205,11 +206,12 @@ GEM
       jekyll (~> 3.5)
       jekyll-feed (~> 0.9)
       jekyll-seo-tag (~> 2.1)
-    minitest (5.11.3)
-    multipart-post (2.0.0)
-    nokogiri (1.10.4)
+    minitest (5.14.1)
+    multipart-post (2.1.1)
+    nokogiri (1.10.9)
       mini_portile2 (~> 2.4.0)
-    octokit (4.9.0)
+    octokit (4.18.0)
+      faraday (>= 0.9)
       sawyer (~> 0.8.0, >= 0.5.3)
     pathutil (0.16.1)
       forwardable-extended (~> 2.6)
@@ -220,30 +222,30 @@ GEM
       ffi (>= 0.5.0, < 2)
     ref (2.0.0)
     rouge (2.2.1)
-    ruby-enum (0.7.2)
+    ruby-enum (0.8.0)
       i18n
     ruby_dep (1.5.0)
-    rubyzip (1.2.1)
+    rubyzip (2.3.0)
     safe_yaml (1.0.4)
     sass (3.5.6)
       sass-listen (~> 4.0.0)
     sass-listen (4.0.0)
       rb-fsevent (~> 0.9, >= 0.9.4)
       rb-inotify (~> 0.9, >= 0.9.7)
-    sawyer (0.8.1)
-      addressable (>= 2.3.5, < 2.6)
-      faraday (~> 0.8, < 1.0)
+    sawyer (0.8.2)
+      addressable (>= 2.3.5)
+      faraday (> 0.8, < 2.0)
     terminal-table (1.8.0)
       unicode-display_width (~> 1.1, >= 1.1.1)
     therubyracer (0.12.3)
       libv8 (~> 3.16.14.15)
       ref
     thread_safe (0.3.6)
-    typhoeus (1.3.0)
+    typhoeus (1.4.0)
       ethon (>= 0.9.0)
-    tzinfo (1.2.5)
+    tzinfo (1.2.7)
       thread_safe (~> 0.1)
-    unicode-display_width (1.3.3)
+    unicode-display_width (1.7.0)
 
 PLATFORMS
   ruby
@@ -255,4 +257,4 @@ DEPENDENCIES
   therubyracer
 
 BUNDLED WITH
-   1.16.2
+   2.1.2