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<meta name="description" content=" Image Content So, you want to put stuff in your container? This is understandable. There are a few ways to do that, some of which are more reproducible than others.BootstrapWe recommend strongly that you add content during an image bootstrap, because the operations on your image will be recorded in the build specification file, and you’ll remember. During bootstrap you can get content: by way of Docker layers by cloning a Github (or other) repository in the %post section using wget, curl, or any other method to download in %post or %setup Adding pairs of path/on/host /path/in/container to the %files sectionAfter BootstrapWhile we don’t recommend these methods (this is not reproducible practice) there are ways to add content after image creation.Writable ShellYou can shell into your image with --writable and then issue any kind of content creation, or download using wget or curl or git clone, etc.CopySingularity has a copy command that is basically a wrapper around the system’s /bin/cp. This means that it accepts all of the same arguments, and option flags and you should look at these:man cpNotably, you might run into the issue of copying a file to your container, and then you can’t execute it. This is because you need to use -p to preserve permissions:singularity copy container.img -p /path/host/script.sh /binDone without sudo, the permissions might look something like this:$ singularity exec container.img ls -l /bin/script.sh-rwxrwxr-x 1 vanessa vanessa 11 Apr 13 16:07 /bin/script.shIf you want to change the owner to root, you can do that first:$ chmod 775 script.sh$ sudo chown root script.sh$ sudo singularity copy container.img -p script.sh /bin$ singularity exec container.img ls -l /bin/script.sh-rwxrwxr-x 1 root vanessa 11 Apr 13 16:07 /bin/script.sh$ singularity exec rosdep.img /bin/script.shHelloMountMount is useful for physically mounting a container (it may not even be working) and moving files around.mkdir mnt $ singularity mount centos7.img mntcentos7.img is mounted at: mntSpawning a new shell in this namespace, to unmount, exit shellSingularity: \w> Note that if you run without sudo you won’t see any files in the folder. You must run with sudo for them to be viewable.mkdir mnt $ sudo singularity mount centos7.img mntcentos7.img is mounted at: mnt$A key difference is that with sudo, it creates the mount and doesn’t shell. But even with sudo, you can’t copy files. The container is read only.$ cp file.sh mnt/bin/cp: cannot create regular file 'mnt/bin/file.sh': Read-only file system$ sudo cp file.sh mnt/bin/cp: cannot create regular file 'mnt/bin/file.sh': Read-only file systemNow if we try with sudo and --writablesudo singularity mount --writable centos7.img mntcentos7.img is mounted at: mnt$ sudo cp file.sh mnt/binDoes the file execute from outside the container?ls -l mnt/bin/file.sh-rw-r--r-x 1 root root 13 Apr 13 15:46 mnt/bin/file.shls -l file.sh-rw-rw-r-x 1 vanessa vanessa 13 Apr 13 15:43 file.sh./mnt/bin/file.shhelloYep. And actually, using mount instead of copy seems to better preserve (most) of the file’s attributes. We can do a bit better, however:ls -l mnt/bin/file.sh-rw-rw-r-x 1 vanessa vanessa 13 Apr 13 15:43 mnt/bin/file.shWe generally recommend that you do not manually move things. It’s not good practice. Previous Next Edit me Site last generated: Jul 26, 2017 ">
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<p>So, you want to put stuff in your container? This is understandable. There are a few ways to do that, some of which are more reproducible than others.</p>
<h2 id="bootstrap">Bootstrap</h2>
<p>We recommend strongly that you add content during an image <a href="/docs-bootstrap">bootstrap</a>, because the operations on your image will be recorded in the build specification file, and you’ll remember. During bootstrap you can get content:</p>
<ul>
<li>by way of Docker layers</li>
<li>by cloning a Github (or other) repository in the <code class="highlighter-rouge">%post</code> section</li>
<li>using wget, curl, or any other method to download in <code class="highlighter-rouge">%post</code> or <code class="highlighter-rouge">%setup</code></li>
<li>Adding pairs of <code class="highlighter-rouge">path/on/host</code> <code class="highlighter-rouge">/path/in/container</code> to the <code class="highlighter-rouge">%files</code> section</li>
</ul>
<h2 id="after-bootstrap">After Bootstrap</h2>
<p>While we don’t recommend these methods (this is not reproducible practice) there are ways to add content after image creation.</p>
<h3 id="writable-shell">Writable Shell</h3>
<p>You can shell into your image with <code class="highlighter-rouge">--writable</code> and then issue any kind of content creation, or download using <code class="highlighter-rouge">wget</code> or <code class="highlighter-rouge">curl</code> or <code class="highlighter-rouge">git clone</code>, etc.</p>
<h3 id="copy">Copy</h3>
<p>Singularity has a <code class="highlighter-rouge">copy</code> command that is basically a wrapper around the system’s <code class="highlighter-rouge">/bin/cp</code>. This means that it accepts all of the same arguments, and option flags and you should look at these:</p>
<div class="highlighter-rouge"><pre class="highlight"><code>man cp
</code></pre>
</div>
<p>Notably, you might run into the issue of copying a file to your container, and then you can’t execute it. This is because you need to use <code class="highlighter-rouge">-p</code> to preserve permissions:</p>
<div class="highlighter-rouge"><pre class="highlight"><code>singularity copy container.img -p /path/host/script.sh /bin
</code></pre>
</div>
<p>Done without sudo, the permissions might look something like this:</p>
<div class="highlighter-rouge"><pre class="highlight"><code>$ singularity exec container.img ls -l /bin/script.sh
-rwxrwxr-x 1 vanessa vanessa 11 Apr 13 16:07 /bin/script.sh
</code></pre>
</div>
<p>If you want to change the owner to root, you can do that first:</p>
<div class="highlighter-rouge"><pre class="highlight"><code>$ chmod 775 script.sh
$ sudo chown root script.sh
$ sudo singularity copy container.img -p script.sh /bin
$ singularity exec container.img ls -l /bin/script.sh
-rwxrwxr-x 1 root vanessa 11 Apr 13 16:07 /bin/script.sh
$ singularity exec rosdep.img /bin/script.sh
Hello
</code></pre>
</div>
<h3 id="mount">Mount</h3>
<p>Mount is useful for physically mounting a container (it may not even be working) and moving files around.</p>
<div class="highlighter-rouge"><pre class="highlight"><code>mkdir mnt
$ singularity mount centos7.img mnt
centos7.img is mounted at: mnt
Spawning a new shell in this namespace, to unmount, exit shell
Singularity: \w>
</code></pre>
</div>
<p>Note that if you run <strong>without</strong> sudo you won’t see any files in the folder. You must run with sudo for them to be viewable.</p>
<div class="highlighter-rouge"><pre class="highlight"><code>mkdir mnt
$ sudo singularity mount centos7.img mnt
centos7.img is mounted at: mnt
$
</code></pre>
</div>
<p>A key difference is that with sudo, it creates the mount and doesn’t shell. But even with sudo, you can’t copy files. The container is read only.</p>
<div class="highlighter-rouge"><pre class="highlight"><code>$ cp file.sh mnt/bin/
cp: cannot create regular file 'mnt/bin/file.sh': Read-only file system
$ sudo cp file.sh mnt/bin/
cp: cannot create regular file 'mnt/bin/file.sh': Read-only file system
</code></pre>
</div>
<p>Now if we try with sudo and <code class="highlighter-rouge">--writable</code></p>
<div class="highlighter-rouge"><pre class="highlight"><code>sudo singularity mount --writable centos7.img mnt
centos7.img is mounted at: mnt
$ sudo cp file.sh mnt/bin
</code></pre>
</div>
<p>Does the file execute from outside the container?</p>
<div class="highlighter-rouge"><pre class="highlight"><code>ls -l mnt/bin/file.sh
-rw-r--r-x 1 root root 13 Apr 13 15:46 mnt/bin/file.sh
ls -l file.sh
-rw-rw-r-x 1 vanessa vanessa 13 Apr 13 15:43 file.sh
./mnt/bin/file.sh
hello
</code></pre>
</div>
<p>Yep. And actually, using <code class="highlighter-rouge">mount</code> instead of <code class="highlighter-rouge">copy</code> seems to better preserve (most) of the file’s
attributes. We can do a bit better, however:</p>
<div class="highlighter-rouge"><pre class="highlight"><code>ls -l mnt/bin/file.sh
-rw-rw-r-x 1 vanessa vanessa 13 Apr 13 15:43 mnt/bin/file.sh
</code></pre>
</div>
<p>We generally recommend that you do not manually move things. It’s not good practice.</p>
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