Merge pull request #797 from NeuroDesk/brainnetviewer

recipes/brainnetviewer/README.md

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+
+----------------------------------
+## brainnetviewer/toolVersion##
+
+BrainNet Viewer is a brain network visualization tool, which can help researchers to visualize structural and functional connectivity patterns from different levels in a quick, easy, and flexible way.
+
+**Citation:** Xia M, Wang J, He Y. BrainNet Viewer: a network visualization tool for human brain connectomics. PLoS One. 2013 Jul 4;8(7):e68910. doi: 10.1371/journal.pone.0068910. PMID: 23861951; PMCID: PMC3701683.
+
+**Homepage:** https://www.nitrc.org/projects/bnv/
+
+**Example:** `brainnetviewer`
+
+**License:** GNU General Public License Version 3 (GPL-3.0)
+
+----------------------------------

recipes/brainnetviewer/bnv.star

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+bnv_binaries = "https://www.nitrc.org/frs/download.php/11585/BrainNetViewer20191031_sd_Linux_x64_compiled2018a.zip"
+mcr_installer = "https://ssd.mathworks.com/supportfiles/downloads/R2018a/deployment_files/R2018a/installers/glnxa64/MCR_R2018a_glnxa64_installer.zip"
+
+mcr_installed = define.build_vm(
+    directives = [
+        define.plan(
+            builder = "ubuntu@jammy",
+            packages = [
+                query("openjdk-17-jdk"),
+                query("bash"),
+            ],
+            tags = ["level3", "defaults"],
+        ),
+        directive.archive(define.read_archive(define.fetch_http(mcr_installer), ".zip"), target = "/mcr"),
+        directive.run_command("/mcr/install -destinationFolder /opt/matlab -mode silent -agreeToLicense yes"),
+        directive.run_command("tar caf /matlab.tar.gz /opt/matlab"),
+    ],
+    storage_size = 16 * 1024,
+    output = "/matlab.tar.gz",
+)
+
+mcr_installed_archive = define.read_archive(mcr_installed, ".tar.gz")
+
+bnv_root = define.build_fs([
+    define.plan(
+        builder = "ubuntu@jammy",
+        packages = [
+            query("openjdk-17-jdk"),
+            query("bash"),
+        ],
+        tags = ["level3", "defaults", "noScripts"],
+    ),
+    mcr_installed_archive,
+    directive.builtin("init", "/init"),
+    define.read_archive(define.fetch_http(bnv_binaries), ".zip"),
+], "tar")

recipes/brainnetviewer/brainnetviewer

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+#!/bin/bash
+
+exec /run_BrainNet.sh /opt/matlab/v94 $@

recipes/brainnetviewer/build.sh

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+#!/usr/bin/env bash
+set -e
+
+export toolName='brainnetviewer'
+export toolVersion='1.7.20191031'
+
+if [ "$1" != "" ]; then
+    echo "Entering Debug mode"
+    export debug=$1
+fi
+
+source ../main_setup.sh
+
+# Use Singlrity/Apptainer to run TinyRange to generate the rootfs.
+singularity run docker://ghcr.io/tinyrange/tinyrange:stable build bnv.star:bnv_root -o bnv.tar
+
+# Make sure the automaticcly included template doesn't add to the final layer.
+neurodocker generate ${neurodocker_buildMode} \
+    --base-image ubuntu \
+    --pkg-manager apt \
+    --base-image scratch \
+    --add bnv.tar . \
+    --run "/init -run-scripts /.pkg/scripts.json" \
+    --run="printf '#!/bin/bash\nls -la' > /usr/bin/ll" \
+    --run="chmod +x /usr/bin/ll" \
+    --run="mkdir -p ${mountPointList}" \
+    --copy brainnetviewer /usr/bin/brainnetviewer \
+    --entrypoint "/usr/bin/brainnetviewer" \
+    --env DEPLOY_BINS=brainnetviewer \
+    --copy README.md /README.md \
+ > ${imageName}.${neurodocker_buildExt}
+
+if [ "$1" != "" ]; then
+   ./../main_build.sh
+fi