Merge pull request #214 from bagashe/release-0.7.0

Prep for release 0.7.0

Author: bagashe

.github/workflows/Build.yml

@@ -17,8 +17,8 @@ jobs:
         lsb_release -a
         mkdir shasta-build
         cd shasta-build 
-        cmake .. -DBUILD_ID="Shasta unreleased test build newer than release 0.6.0 at commit "$GITHUB_SHA
-        # cmake .. -DBUILD_ID="Shasta Release 0.6.0" 
+        # cmake .. -DBUILD_ID="Shasta unreleased test build newer than release 0.7.0 at commit "$GITHUB_SHA
+        cmake .. -DBUILD_ID="Shasta Release 0.7.0" 
         make -j 2 all
         make install/strip
         mv shasta-install shasta-Ubuntu-20.04
@@ -50,8 +50,8 @@ jobs:
         mkdir shasta-build
         cd shasta-build 
         cmake .. -DBUILD_DYNAMIC_EXECUTABLE=OFF -DBUILD_DYNAMIC_LIBRARY=OFF -DBUILD_WITH_HTTP_SERVER=OFF \
-          -DBUILD_ID="Shasta unreleased test build newer than release 0.6.0 at commit "$GITHUB_SHA
-        # cmake .. -DBUILD_ID="Shasta Release 0.6.0" 
+          -DBUILD_ID="Shasta unreleased test build newer than release 0.7.0 at commit "$GITHUB_SHA
+        # cmake .. -DBUILD_ID="Shasta Release 0.7.0" 
         make -j 2 all
         make install/strip
         mv shasta-install shasta-Ubuntu-20.04
@@ -74,8 +74,8 @@ jobs:
       run: |
         mkdir shasta-build
         cd shasta-build 
-        cmake .. -DBUILD_ID="Shasta unreleased test build for MacOS-10.15 newer than release 0.6.0 at commit "$GITHUB_SHA
-        # cmake .. -DBUILD_ID="Shasta Release 0.6.0 for MacOS"
+        # cmake .. -DBUILD_ID="Shasta unreleased test build for MacOS-10.15 newer than release 0.7.0 at commit "$GITHUB_SHA
+        cmake .. -DBUILD_ID="Shasta Release 0.7.0 for MacOS"
         make VERBOSE=1 -j 2 all
         make install/strip
         # See what libraries the executable depends on.

docs/MakeRelease.html

@@ -29,17 +29,14 @@ <h1>Creating a new release</h1>
 <li>In 
 <code>shasta/.github/workflows/Build.yml</code>,
 change <code>BUILD_ID</code> to <code>Shasta Release X.Y.Z</code>
-in all <code>cmake</code> commands (5 instances at the time of last update of this documentation).
+in all <code>cmake</code> commands (3 instances at the time of last update of this documentation).
 <li>Commit and push this change to trigger a new build on GitHub Actions.
 Wait for that build to complete.
-<li>Download the 6 artifacts. Unzip them and rename them to the following:
+<li>Download the 3 artifacts. Unzip them and rename them to the following:
 <ul>
 <li><code>shasta-Linux-X.Y.Z</code>
-<li><code>shasta-OldLinux-X.Y.Z</code> 
 <li><code>shasta-macOS-X.Y.Z</code>
 <li><code>shasta-Ubuntu-20.04-X.Y.Z.tar</code>
-<li><code>shasta-Ubuntu-18.04-X.Y.Z.tar</code>
-<li><code>shasta-Ubuntu-16.04-X.Y.Z.tar</code>
 </ul>
 <li> Build Shasta for 64-bit ARM (<code>aarch64</code>). Github Actions currently don't support <code>aarch64</code> containers. So the easiest way to do this is on a Graviton2 ec2 instance in AWS. On an <code>aarch64</code> instance running Ubuntu 20.04 LTS, do the following:
 <ul>
@@ -78,7 +75,7 @@ <h1>Creating a new release</h1>
 change <code>BUILD_ID</code> to 
 <code>Shasta unreleased test build newer than release X.Y.Z</code>
 in all <code>cmake</code> commands for future GitHub Actions builds
-(5 instances at the time of last update of this documentation).
+(3 instances at the time of last update of this documentation).
 </ul>
 
 

docs/QuickStart.html

@@ -21,13 +21,13 @@ <h2 id="QuickStartLinux">Linux</h2>
 You can use the following commands to download the executable from the latest release and run an assembly:
 <pre>
 # Download the executable for the latest release.
-curl -O -L https://github.com/chanzuckerberg/shasta/releases/download/0.6.0/shasta-Linux-0.6.0
+curl -O -L https://github.com/chanzuckerberg/shasta/releases/download/0.7.0/shasta-Linux-0.7.0
 
 # Grant necessary permissions.
-chmod ugo+x shasta-Linux-0.6.0
+chmod ugo+x shasta-Linux-0.7.0
 
 # Run an assembly.
-./shasta-Linux-0.6.0 --input input.fasta
+./shasta-Linux-0.7.0 --input input.fasta
 </pre>
 
 <p>
@@ -67,13 +67,13 @@ <h2 id="QuickStartMacOS">macOS</h2>
 
 <pre>
 # Download the executable for the latest release.
-curl -O -L https://github.com/chanzuckerberg/shasta/releases/download/0.6.0/shasta-macOS-0.6.0
+curl -O -L https://github.com/chanzuckerberg/shasta/releases/download/0.7.0/shasta-macOS-0.7.0
 
 # Grant necessary permissions.
-chmod ugo+x shasta-macOS-0.6.0
+chmod ugo+x shasta-macOS-0.7.0
 
 # Run an assembly.
-./shasta-macOS-0.6.0 --input input.fasta
+./shasta-macOS-0.7.0 --input input.fasta
 </pre>
 The macOS executable has been tested on macOS 10.15 (<i>Catalina</i>) and
 macOS 10.14 (<i>Mojave</i>).

docs/Running.html

@@ -188,7 +188,7 @@ <h2 id=LowMemory>Running with less than optimal memory</h2>
 there is one core for each virtual processor.
 <li>A Shasta executable for ARM is currenly not available
 with any Shasta release but can be built from source.
-It will be first available with Shasta Release 0.6.0.
+It will be first available with Shasta Release 0.7.0.
 </ul>
 
 <table>
@@ -649,12 +649,6 @@ <h2 id=Docker>Running an assembly using Docker</h2>
 
 <h2 id=Errors>Dealing with errors</h2>
 <ul>
-<li> <code>FATAL: kernel too old</code> : If you get this error when using
-<code>shasta-Linux-0.6.0</code>, then you should retry with <code>shasta-OldLinux-0.6.0</code>, which is a version of Shasta built for older kernels.
-You can find out the kernel version on your system by running <code>uname -a</code>.
-Compare it with the minimum required kernel version for the Shasta executable by running
-<code>file shasta-Linux-0.6.0</code> or <code>file shasta-OldLinux-0.6.0</code>.
-
 <li> <code>sh: 1: cannot create /sys/kernel/mm/hugepages/hugepages-2048kB/nr_overcommit_hugepages: Read-only file system</code>: Shasta needs root privilege to use the `hugetlbfs` filesystem. If you're running this in a Docker container, you need to
 use the Docker option <code>--privileged</code>.  	
 </ul>