At this point, you are comfortable with preview or install of a SCIF, and are ready for more advanced interaction. This means any of the following commands, and some of these have already been demonstrated in the previous tutorial, and will have detail added here:

• apps: list apps installed in a SCIF or recipe (or dump)
• inspect: look at details for one or more apps
• pyshell: interactive python shell to explore a SCIF or recipe
• shell: interactive shell to explore a SCIF
• run: run an app runscript, or default to shell in app context
• exec: execute a command to an app with context active

Apps

Apps will give you a simple listing of apps installed.

$ scif apps
SCIF [app]              [root]
1  hello-world-script	/scif/apps/hello-world-script
2  hello-world-echo	/scif/apps/hello-world-echo

and if you don’t have any installed, you get a warning instead.

WARNING /scif is not detected as a recipe or base.

Inspect

Inspect is what you want to use to look at different metadata about a SCIF or app within it. Without any arguments, you will get json output for all apps installed in your SCIF:

scif inspect 
{
    "hello-world-script": {
        "appinstall": [
            "echo \"echo 'Hello World!'\" >> $SCIF_APPBIN/hello-world.sh",
            "chmod u+x $SCIF_APPBIN/hello-world.sh"
        ],
        "appenv": [
            "THEBESTAPP $SCIF_APPNAME"
        ],
        "apprun": [
            "/bin/bash hello-world.sh"
        ]
    },
    "hello-world-echo": {
        "appenv": [
            "THEBESTAPP $SCIF_APPNAME"
        ],
        "apprun": [
            "echo \"The best app is $THEBESTAPP\""
        ]
    }
}

If you add the name of an app, you will filter the output to it:

scif inspect hello-world-echo
{
    "hello-world-echo": {
        "appenv": [
            "THEBESTAPP $SCIF_APPNAME"
        ],
        "apprun": [
            "echo \"The best app is $THEBESTAPP\""
        ]
    }
}

If you add a particular attribute, you can further filter the result. For attributes your choices are a (all) l (labels) e (environment) r (runscript) f (files) or i (install). Here we ask to see the runscript (r)

scif inspect hello-world-echo r
{
    "hello-world-echo": {
        "apprun": [
            "echo \"The best app is $THEBESTAPP\""
        ]
    }
}

Finally, to dump the original recipe, just use “dump”:

scif dump
%appinstall
echo "echo 'Hello World!'" >> $SCIF_APPBIN/hello-world.sh
chmod u+x $SCIF_APPBIN/hello-world.sh

%appenv
THEBESTAPP $SCIF_APPNAME

%apprun
/bin/bash hello-world.sh

%appenv
THEBESTAPP $SCIF_APPNAME

%apprun
echo "The best app is $THEBESTAPP"

Pyshell

Pyshell produces an interactive python terminal to work with your SCIF. As we saw previously, depending on whether you provide a recipe, an app, or both, you get different environments to work in. This is entry to a python interactive shell.

SCIF python shell Options

If you want to change the default shell used, set the variable SCIF_SHELL. For default it will use /bin/bash.

Shell

Running a standard shell means bash in the context of an app, meaning a subprocess for /bin/bash (default determined by the environment variable SCIF_PYSHELL during runtime). We aren’t in any sort of container, so there is no context of shell in the way you would think of shelling into a container or running SSH to connect to a server. This is entry to a bash shell.

SCIF shell Options

From the above, we can see that it’s possible to shell into only a context, meaning the context of an installed app, or the entire filesystem. Physically shelling into a recipe (a file system that doesn’t exist yet) doesn’t make sense.

Special Command Stickers

The Scientific Filesystem has some special command stickers that (as is true to their name) will stick with your commands and not get lost due to parsing by the host. For any command (e.g., run, exec) for which you are passing commands from the host to the SCIF, it sometimes can be troublesome if a variable gets evaluated on the host that needs to be evaluated in a container with SCIF, for example. To handle this, we have a small set of variables that are passed in, and evaluated internally or relative to the SCIF.

If you are having trouble with a command and you’ve tried quotes, these stickers might be exactly what you need! If there is another command being parsed that you want help with, let us know.

Run

The run command will explicity run the script provided in the apprun section. In our example, running hello-world-echo will echo “Hello World” to the console.

$ scif run hello-world-echo
[hello-world-echo] executing /bin/bash /scif/apps/hello-world-echo/scif/runscript
The best app is hello-world-echo

Running the second app, hello-world-script, is actually a very cool example because in it we are calling a script that was written via an echo during the install step. If you remember:

%appinstall hello-world-script
    echo "echo 'Hello World!'" >> $SCIF_APPBIN/hello-world.sh
    chmod u+x $SCIF_APPBIN/hello-world.sh

and then running it:

%apprun hello-world-script
    /bin/bash hello-world.sh

This means the following:

• we have the variable SCIF_APPBIN on the path for our usage during install.
• we also have the SCIF_APPBIN added to the PATH for runtime, so the script is found period.

Awesome!

If an app doesn’t have an %apprun section, we default to a shell. For example, here is a third app that I added to install that is just an environment

%appenv hello-world-env
    OMG=TACOS

# then scif install hello-world.scif again

scif install hello-world.scif hello-world-env
Installing base at /scif
+ appenv hello-world-env

if we run the app, we get a shell.

$ scif run hello-world-env
[hello-world-env] executing /bin/bash 
$/scif/apps/hello-world-env# echo $OMG
TACOS

Again, cool! This example also nicely shows how an entire app can just be an environment context. Now it’s time to look at executing commands with “exec.”

Exec

Let’s take the hello-world-echo app as an example. When we shell with context of this app, we would expect its environment variables to be active. Can we show that with exec?

$ scif exec hello-world-echo echo The best app is $THEBESTAPP
[hello-world-echo] executing /bin/echo
The best app is 

Ruhroh! No output! The reason is because the variable gets evaluated before getting parsed in. To get around this, we have a special syntax to distinguish an environment variable. Try this!

$ scif exec hello-world-echo echo The best app is [e]THEBESTAPP
[hello-world-echo] executing /bin/echo The best app is $THEBESTAPP
The best app is hello-world-echo

This little bug has always been a pet peeve of mine, so I’ve introduced the little [e] so we don’t have to struggle.

More coming soon!