Working on resolving issue #17

files/ansible_playbook_ec2.yml

@@ -5,25 +5,25 @@
 #
 # If other VMs are running then you'll need to do something smarter.
 #
-- hosts: training_vm
+- hosts: tag_Role_training_snakemake
   become: yes
   become_user: training
   tasks:
 
     - name: Set alternative password for VNC
       vars:
         passwd: "ed-dash-vnc"
-      become_user: training
       shell:
         executable: /bin/bash
-        chdir: /home/training/.vnc
+        chdir: ~/.vnc
         cmd: |
              set -euo pipefail
+             cd ~
              mv passwd passwd.old
              echo '{{ passwd }}' | /opt/tigervnc/usr/bin/vncpasswd -f > passwd
              chmod 0600 passwd
       args:
-        creates: /home/training/.vnc/passwd.old
+        creates: ~/.vnc/passwd.old
       when: false # rule is disabled for now
 
     # This one runs as root. The conda-forge versions of these packages are problematic
@@ -47,69 +47,66 @@
     - name: Fetch Miniconda Installer
       get_url:
         url: https://repo.anaconda.com/miniconda/Miniconda3-py39_4.9.2-Linux-x86_64.sh
-        dest: /home/training/Downloads/miniconda3_installer.sh
+        dest: "~/Downloads/miniconda3_installer.sh"
         mode: '0644'
         checksum: sha256:536817d1b14cb1ada88900f5be51ce0a5e042bae178b5550e62f61e223deae7c
 
     - name: Run Miniconda Installer
       shell:
         executable: /bin/bash
-        chdir: /home/training
         cmd: |
              set -euo pipefail
              rm -rf ~/.conda ~/miniconda3
-             bash ./Downloads/miniconda3_installer.sh -b
+             bash ~/Downloads/miniconda3_installer.sh -b
              source ~/miniconda3/bin/activate
              conda init
-        creates: /home/training/.conda/environments.txt
+        creates: ~/.conda/environments.txt
 
     # I could do a full checkout of the GitHub repo here?
     # No checksum - the file may change
     - name: Download conda env spec
       get_url:
-        url: https://raw.githubusercontent.com/carpentries-incubator/snakemake-novice-bioinformatics/gh-pages/files/conda_env_min.yaml
-        dest: /home/training/Downloads/snakemake_conda_env.yaml
+        url: https://raw.githubusercontent.com/carpentries-incubator/snakemake-novice-bioinformatics/gh-pages/files/conda_env.yaml
+        dest: "~/Downloads/snakemake_conda_env.yaml"
         mode: '0644'
         backup: yes
 
     - name: Bootstrap deps into base env
       shell:
         executable: /bin/bash
-        chdir: /home/training
         cmd: |
              set -euo pipefail
              source ~/miniconda3/bin/activate
-             conda env update -n base --file /home/training/Downloads/snakemake_conda_env.yaml
+             conda env update -n base --file ~/Downloads/snakemake_conda_env.yaml
              snakemake --version
-        creates: /home/training/miniconda3/bin/snakemake
+        creates: "~/miniconda3/bin/snakemake"
 
     - name: Download the data files
       get_url:
-        url: https://ndownloader.figshare.com/files/28531743
-        dest: /home/training/Downloads/snakemake_data.tar.gz
+        url: https://ndownloader.figshare.com/files/35058796
+        dest: "~/Downloads/snakemake_data.tar.gz"
         mode: '0644'
         backup: no
 
     - name: Unpack the data files
       unarchive:
-        src: /home/training/Downloads/snakemake_data.tar.gz
-        dest: /home/training
+        src: "~/Downloads/snakemake_data.tar.gz"
+        dest: "~"
         remote_src: yes
         extra_opts: [ --strip-components=1 ]
-        creates: /home/training/yeast
+        creates: "~/yeast"
 
-    # I didn't realise GG GZipped all the reads. I can probably work with this but for
-    # the initial run-through I'll stick with the unpacked version.
+    # I didn't realise GG GZipped all the reads. This re-unzips them.
+    # Redundant since I actually fixed the tarball.
     - name: Fix up the data files
       shell:
         executable: /bin/bash
-        chdir: /home/training
         cmd: |
              set -euo pipefail
              cd ~
              gunzip yeast/reads/*.gz
              rm -rf yeast/bams
              rm -f yeast/samples.csv
              rm -f yeast/.*.txt
-        creates: /home/training/yeast/reads/ref1_1.fq
+        creates: "~/yeast/reads/ref1_1.fq"
 

files/conda_env_min.yaml → files/conda_env.yaml

@@ -20,7 +20,6 @@ dependencies:
   - c-ares=1.17.1=h7f98852_1
   - cachetools=4.2.2=pyhd8ed1ab_0
   - cairo=1.16.0=h6cf1ce9_1008
-  - certifi=2021.10.8=py39hf3d152e_0
   - cffi=1.14.5=py39he32792d_0
   - chardet=4.0.0=py39hf3d152e_1
   - click=7.1.2=pyh9f0ad1d_0
@@ -68,6 +67,7 @@ dependencies:
   - google-resumable-media=1.2.0=pyhd3deb0d_0
   - googleapis-common-protos=1.53.0=py39hf3d152e_0
   - graphite2=1.3.13=h58526e2_1001
+  - graphicsmagick=1.3.26=hf0fcf2e_2
   - graphviz=2.42.3=h0511662_0
   - grpcio=1.37.1=py39hff7568b_0
   - harfbuzz=2.8.1=h83ec7ef_0

setup.md

@@ -21,7 +21,7 @@ To prepare for the course:
 * Download and unpack [the sample dataset tarball](https://ndownloader.figshare.com/files/35058796)
 * Install software packages, including Snakemake and the bioinformatics tools, via Conda:
   * If you don't already have Conda, get [the Miniconda installer](https://docs.conda.io/en/latest/miniconda.html) and follow instructions
-  * Get [the environment file](files/conda_env_all.yaml) and run `conda env update --file conda_env_all.yaml`
+  * Get [the environment file](files/conda_env.yaml) and run `conda env update --file conda_env.yaml`
   * Ensure the right environment is active - `conda activate snakemake_dash`
 * Set up the GEdit or Nano text editor (other text editors will work fine but we only provide specific setup instructions
   for GEdit and Nano).
@@ -44,7 +44,7 @@ The following settings are also recommended:
 * Set the Syntax to "Python3", rather than "Plain Text"
 * Set Tab width to 4
 * Enable automatic indentation
-* Hilight matching brackets
+* Highlight matching brackets
 * Display line numbers
 
 ### Nano