Rename topic

This fixes the error:
    Resource not found: /topics/aws/README

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>

1 files changed, 0 insertions, 210 deletions

diff --git a/topics/aws/README.gmi b/topics/aws/README.gmi
deleted file mode 100644
index 41981dc..0000000
--- a/topics/aws/README.gmi
+++ /dev/null
@@ -1,210 +0,0 @@
-# Amazon Web Services
-
-## Create a virtual machine
-
-In the browser:
-
-- Log in to Amazon Web Services as "Root user" (https://signin.aws.amazon.com/)
-- Click "Launch a virtual machine"
-- Select instance's O.S. and type
-- Create a key pair to securely connect to the instance
-- Download the created key pair (file `chosen_name.pem`)
-- Allow HTTPS/HTTP traffic from the internet
-- Click "Launch instance"
-
-In the local machine:
-
-```shell
-chmod 400 chosen_name.pem` # ensure your key is not publicly viewable
-ssh -i "chosen_name.pem" ubuntu@ec2-54-211-237-62.compute-1.amazonaws.com` # connect to the instance (the address changes every time the machine is restarted)
-```
-
-Note: select the instance and then click 'Instance state' and 'Stop Instance' to stop it.
-
-## Create multiple users
-
-In the virtual machine:
-
-```shell
-ssh -i "chosen_name.pem" ubuntu@ec2-54-211-237-62.compute-1.amazonaws.com # connect to the virtual machine
-sudo adduser user1 # create a new user
-sudo adduser user2 # create a new user
-sudo sed 's/^PasswordAuthentication no/PasswordAuthentication yes/' /etc/ssh/sshd_config -i # allow new users to use SSH with password authentication
-sudo systemctl restart sshd # restart the SSH service to apply the changes
-```
-
-## Clone a virtual machine
-
-- Select the instance
-- Click "Actions", "Image and templates", and "Create image"
-- Set "Image name" and click "Create image"
-- Click Images->"Create AMI in the menu on the left side
-- Select the AMI and click the "Launch instances from AMI" button
-
-## Set up a pangenomic virtual machine
-
-```shell
-sudo apt-get update
-sudo apt-get upgrade
-sudo apt-get install -y \
-                    git \
-                    bash \
-                    cmake \
-                    make \
-                    g++-11 \
-                    python3-dev \
-                    pybind11-dev \
-                    libbz2-dev \
-                    bc \
-                    libatomic-ops-dev \
-                    autoconf \
-                    libgsl-dev \
-                    zlib1g-dev \
-                    libzstd-dev \
-                    libjemalloc-dev \
-                    libhts-dev \
-                    build-essential \
-                    pkg-config \
-                    time \
-                    curl \
-                    pigz \
-                    tabix \
-                    bcftools \
-                    samtools \
-                    wget \
-                    pip \
-                    libcairo2-dev \
-                    unzip \
-                    parallel \
-    && sudo apt-get clean \
-    && sudo apt-get purge  \
-    && sudo rm -rf /var/lib/apt/lists/*
-sudo apt-get autoremove
-
-git clone --recursive https://github.com/waveygang/wfmash \
-    && cd wfmash \
-    && git pull \
-    && git checkout 8ba3c53f327731ca515abd1ef32179f15acb9732 \
-    && git submodule update --init --recursive \
-    && cmake -H. -DCMAKE_BUILD_TYPE=Release -Bbuild && cmake --build build -- -j $(nproc) \
-    && sudo cp build/bin/wfmash /usr/local/bin/wfmash \
-    && cd ../ \
-    && rm -rf wfmash
-
-git clone --recursive https://github.com/ekg/seqwish \
-    && cd seqwish \
-    && git pull \
-    && git checkout d9e7ab59e73258f57875f2a060437735a460475e \
-    && git submodule update --init --recursive \
-    && cmake -H. -DCMAKE_BUILD_TYPE=Release -Bbuild && cmake --build build -- -j $(nproc) \
-    && sudo cp bin/seqwish /usr/local/bin/seqwish \
-    && cd ../ \
-    && rm -rf seqwish
-
-git clone --recursive https://github.com/pangenome/smoothxg \
-    && cd smoothxg \
-    && git pull \
-    && git checkout 956eb75644522bb2b96b4cca44b7bafa9cf02f4a \
-    && git submodule update --init --recursive \
-    && cmake -H. -DCMAKE_BUILD_TYPE=Release -Bbuild && cmake --build build -- -j $(nproc) \
-    && sudo cp bin/smoothxg /usr/local/bin/smoothxg \
-    && sudo cp deps/odgi/bin/odgi /usr/local/bin/odgi \
-    && cd ../ \
-    && rm -rf odgi
-
-curl https://sh.rustup.rs -sSf | sh -s -- -y
-PATH="$HOME/.cargo/bin:${PATH}"
-
-git clone https://github.com/marschall-lab/GFAffix.git \
-    && cd GFAffix \
-    && git pull \
-    && git checkout 3784c7ee03ee82df576474d2e119fdd88616914b \
-    && cargo install --force --path . \
-    && sudo mv $HOME/.cargo/bin/gfaffix /usr/local/bin/gfaffix \
-    && cd ../ \
-    && rm -rf GFAffix
-
-
-wget https://github.com/vgteam/vg/releases/download/v1.40.0/vg \
-    && chmod +x vg \
-    && sudo mv vg /usr/local/bin/vg
-
-git clone https://github.com/pangenome/vcfbub \
-    && cd vcfbub \
-    && git pull \
-    && git checkout 26a1f0cb216a423f8547c4ad0e0ce38cb9d324b9 \
-    && cargo install --force --path . \
-    && sudo mv $HOME/.cargo/bin/vcfbub /usr/local/bin/vcfbub \
-    && cd ../ \
-    && rm -rf vcfbub
-
-git clone --recursive https://github.com/vcflib/vcflib.git \
-    && cd vcflib \
-    && git checkout 4f2bce873bc520449ec549f36aaaad65bace51ca \
-    && mkdir -p build \
-    && cd build \
-    && cmake -DZIG=OFF -DCMAKE_BUILD_TYPE=Release .. && cmake --build . -- -j $(nproc) \
-    && sudo mv vcfwave /usr/local/bin/vcfwave \
-    && sudo mv vcfuniq /usr/local/bin/vcfuniq \
-    && cd ../../ \
-    && rm -rf vcflib
-
-git clone https://github.com/ekg/fastix.git \
-    && cd fastix \
-    && git pull \
-    && git checkout 331c1159ea16625ee79d1a82522e800c99206834 \
-    && cargo install --force --path . \
-    && sudo mv $HOME/.cargo/bin/fastix /usr/local/bin/fastix \
-    && cd ../ \
-    && rm -rf fastix
-
-git clone https://github.com/ekg/pafplot.git \
-    && cd pafplot \
-    && git pull \
-    && git checkout 7dda24c0aeba8556b600d53d748ae3103ec85501 \
-    && cargo install --force --path . \
-    && sudo mv $HOME/.cargo/bin/pafplot /usr/local/bin/ \
-    && cd ../ \
-    && rm -rf pafplot
-
-pip install igraph==0.10.4
-pip install pycairo==1.23.0
-pip install multiqc==1.14
-sudo mv /home/ubuntu/.local/bin/* /usr/local/bin/
-
-git clone https://github.com/pangenome/pggb.git
-cd pggb
-git checkout de5303e24d3e5594a5a2c9bdeb49aba420b24b0c
-sudo cp pggb /usr/local/bin/pggb
-sudo chmod 777 /usr/local/bin/pggb
-sudo cp partition-before-pggb /usr/local/bin/partition-before-pggb
-sudo chmod 777 /usr/local/bin/partition-before-pggb
-sudo cp scripts/* /usr/local/bin/ # copy required scripts
-
-# Hacky-way to easily get versioning info
-sudo cp -r .git /usr/local/bin/
-git config --global --add safe.directory /usr/local/bin
-cd ..
-rm -rf pggb
-
-# Docker (for Nextflow)
-sudo apt-get remove docker docker-engine docker.io
-sudo apt-get update
-sudo apt install docker.io
-sudo snap install docker
-sudo groupadd docker # create the docker group
-sudo usermod -aG docker ${USER} # add yourself to the docker group
-#  log out and log back in so that your group membership is re-evaluated
-docker run hello-world # test it
-# reboot the instance
-
-# Java 17 (for Nextflow)
-sudo apt install openjdk-17-jre-headless
-
-# Nextflow
-wget -qO- https://get.nextflow.io | bash
-sudo cp nextflow /usr/local/bin/nextflow
-sudo chmod 777 /usr/local/bin/nextflow
-nextflow run nf-core/pangenome -r a_brave_new_world -profile test,docker --outdir a_brave_new_world.output # test it
-nextflow run nf-core/pangenome -r a_brave_new_world --input pggb/data/HLA/DRB1-3123.fa.gz --n_haplotypes 14 --outdir uffa -profile docker -c hla.config # to ask for less resources
-```