Merge branch 'master' of https://github.com/soedinglab/hh-suite

Author: martin-steinegger

.github/workflows/userguide.yml

@@ -0,0 +1,33 @@
+name: Wiki PDF
+
+on:
+  gollum
+
+jobs:
+  build:
+    runs-on: ubuntu-20.04
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          repository: ${{ github.repository }}.wiki
+      - name: Cache
+        uses: actions/cache@v2
+        with:
+          path: |
+            ~/.cache/Tectonic/
+          key: ${{ runner.os }}-${{ env.cache-name }}-tectonic
+      - name: Download pandoc+tectonic
+        run: |
+          wget -qO- https://github.com/tectonic-typesetting/tectonic/releases/download/tectonic%400.3.3/tectonic-0.3.3-x86_64-unknown-linux-gnu.tar.gz | tar xzvf - tectonic
+          wget -qO- https://github.com/jgm/pandoc/releases/download/2.11.3.1/pandoc-2.11.3.1-linux-amd64.tar.gz | tar --strip-components=2 -xzvf - pandoc-2.11.3.1/bin/pandoc
+          sudo mv -f pandoc tectonic /usr/local/bin
+      - name: Build PDF
+        run: |
+          cat Home.md | sed '1,/<!--- TOC END -->/d' | cat .pandoc/meta.yaml - | pandoc --from=markdown --template=.pandoc/eisvogel.tex --toc --pdf-engine tectonic -o userguide.pdf
+      - name: Upload PDF to release assets
+        uses: svenstaro/upload-release-action@483c1e56f95e88835747b1c7c60581215016cbf2
+        with:
+          repo_token: ${{ secrets.GITHUB_TOKEN }}
+          file: userguide.pdf
+          tag: userguide
+          overwrite: true

.travis.yml

@@ -6,8 +6,7 @@
 [![Biocontainer Pulls](https://img.shields.io/endpoint?url=https%3A%2F%2Fmmseqs.com%2Fbiocontainer.php%3Fcontainer%3Dhhsuite)](https://biocontainers.pro/#/tools/hhsuite)
 [![Github All Releases](https://img.shields.io/github/downloads/soedinglab/hh-suite/total.svg)](https://github.com/soedinglab/hh-suite/releases/latest)
 [![Docker Pulls](https://img.shields.io/docker/pulls/soedinglab/hh-suite.svg)](https://hub.docker.com/r/soedinglab/hh-suite)
-[![Travis Build Status](https://travis-ci.org/soedinglab/hh-suite.svg?branch=master)](https://travis-ci.org/soedinglab/hh-suite)
-[![Codeship Status](https://codeship.com/projects/0936c290-2248-0133-bcb4-52bb0fef976f/status?branch=master)](https://codeship.com/projects/96085)
+[![Build Status](https://dev.azure.com/themartinsteinegger/hhsuite/_apis/build/status/soedinglab.hh-suite?branchName=master)](https://dev.azure.com/themartinsteinegger/hhsuite/_build/latest?definitionId=4&branchName=master)
 
 The HH-suite is an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs).
 
@@ -17,7 +16,7 @@ We provide an extensive [user guide](https://github.com/soedinglab/hh-suite/wiki
 
 ### Installation
 
-HH-suite3 can also be installed by downloading a statically compiled version, [conda](https://github.com/conda/conda) or [Docker](https://github.com/moby/moby). HH-suite3 requires a 64-bit system (check with `uname -a | grep x86_64`) with at least the SSE2 instruction set (check by executing `cat /proc/cpuinfo | grep sse2` on Linux or `sysctl -a | grep machdep.cpu.features | grep SSE2` on macOS). `AVX2` is roughly 2x faster compared to SSE2.
+HH-suite3 can also be installed by downloading a statically compiled version, [conda](https://github.com/conda/conda) or [Docker](https://github.com/moby/moby). HH-suite3 requires a 64-bit system (check with `uname -a | grep x86_64`). On AMD/Intel CPUs it requires at least support for the SSE2 instruction set (check by executing `cat /proc/cpuinfo | grep sse2` on Linux or `sysctl -a | grep machdep.cpu.features | grep SSE2` on macOS). `AVX2` is roughly 2x faster compared to SSE2. HH-suite3 also works on Linux systems with ARM64 and PPC64LE CPUs. Precompiled binaries for all supported systems can be found at [mmseqs.com/hhsuite](https://mmseqs.com/hhsuite).
 
 ```
 # install via conda
@@ -53,7 +52,7 @@ export PATH="$(pwd)/bin:$(pwd)/scripts:$PATH"
 :exclamation: To compile HH-suite3 on macOS, first install the `gcc` compiler from [Homebrew](https://brew.sh). The default macOS `clang` compiler does not support OpenMP and HH-suite3 will only be able to use a single thread. Then replace the `cmake` call above with the following one:
 
 ```
-CC="$(brew --prefix)/bin/gcc-8" CXX="$(brew --prefix)/bin/g++-8" cmake -DCMAKE_INSTALL_PREFIX=. ..
+CC="$(brew --prefix)/bin/gcc-10" CXX="$(brew --prefix)/bin/g++-10" cmake -DCMAKE_INSTALL_PREFIX=. ..
 ```