Hello World! This is the getting started example to build a Scentific Filesystem. For maximum reproducibility, we will do this inside a linux container, both Docker and Singularity.
Read more about the specification here Read more about the definition file
The definition file hello-world.scif in this repository is the instruction that will be used to build the SCIF. Whether we are inside Docker or Singularity, we install the scif client as follows:
pip install scif
and you could also install from Github if you want a development version:
git clone https://www.github.com/vsoch/scif.git
cd scif && python setup.py install
The scif is then installed as follows (with root)
scif install hello-world.scif
For the instructions below, we will interact with the scif from inside the containers. If you want examples for interaction from outside of each container, see the official documentation quick start that have more details. If you want to see the Docker and Singularity commands side by side, see the really quick start.
First build your container:
docker build -t vanessa/hello-world-scif .
If you don't know anything, you might execute the container. And then you discover the scif entrypoint to guide you!
docker run hello-world-scif
Scientific Filesystem [v0.0.4]
usage: scif [-h] [--debug] [--quiet] [--writable]
{version,pyshell,shell,preview,help,install,inspect,run,apps,dump,exec}
...
scientific filesystem tools
optional arguments:
-h, --help show this help message and exit
--debug use verbose logging to debug.
--quiet suppress print output
--writable, -w for relevant commands, if writable SCIF is needed
actions:
actions for Scientific Filesystem
{version,pyshell,shell,preview,help,install,inspect,run,apps,dump,exec}
scif actions
version show software version
pyshell Interactive python shell to scientific filesystem
shell shell to interact with scientific filesystem
preview preview changes to a filesytem
help look at help for an app, if it exists.
install install a recipe on the filesystem
inspect inspect an attribute for a scif installation
run entrypoint to run a scientific filesystem
apps list apps installed
dump dump recipe
exec execute a command to a scientific filesystem
List apps
docker run vanessa/hello-world-scif apps
SCIF [app] [root]
1 hello-world /scif/apps/hello-world
Get help for hello world
docker run vanessa/hello-world-scif help hello-world
This is an example "Hello World" application. You can install it to a
Scientific Filesystem (scif) with the command:
scif install hello-world.scif
if you need to install scif:
pip install scif
Run "hello-world"
docker run vanessa/hello-world-scif run hello-world
[hello-world] executing /bin/bash /scif/apps/hello-world/scif/runscript
Hello World!
Execute a command in context of the app "hello world." Notice how we replace the typical $ for the environment variable with [e]
docker run vanessa/hello-world-scif exec hello-world ls [e]SCIF_APPROOT
[hello-world] executing /bin/ls $SCIF_APPROOT
bin
lib
scif
Inspect the hello-world app
docker run vanessa/hello-world-scif inspect hello-world
{
"hello-world": {
"apprun": [
"/bin/bash hello-world.sh"
],
"appinstall": [
"echo \"echo 'Hello World!'\" >> $SCIF_APPBIN/hello-world.sh",
"chmod u+x $SCIF_APPBIN/hello-world.sh"
],
"appenv": [
"THEBESTAPP=$SCIF_APPNAME",
"export THEBESTAPP"
],
"applabels": [
"MAINTAINER Vanessasaur",
"VERSION 1.0"
],
"apphelp": [
"This is an example \"Hello World\" application. You can install it to a",
"Scientific Filesystem (scif) with the command:",
"scif install hello-world.scif",
"if you need to install scif:",
"pip install scif"
]
}
}
Interactively shell into the container in context of the app "hello-world"
docker run -it vanessa/hello-world-scif shell hello-world
[hello-world] executing /bin/bash
root@ddf1ba27fd68:/scif/apps/hello-world# env | grep SCIF_
SCIF_APPMETA=/scif/apps/hello-world/scif
SCIF_DATA=/scif/data
SCIF_APPHELP_hello_world=/scif/apps/hello-world/scif/runscript.help
SCIF_APPDATA=/scif/data/hello-world
THEBESTAPP=$SCIF_APPNAME
SCIF_APPENV=/scif/apps/hello-world/scif/environment.sh
SCIF_APPROOT=/scif/apps/hello-world
SCIF_APPRECIPE_hello_world=/scif/apps/hello-world/scif/hello-world.scif
SCIF_APPDATA_hello_world=/scif/data/hello-world
SCIF_APPLABELS=/scif/apps/hello-world/scif/labels.json
SCIF_APPRUN=/scif/apps/hello-world/scif/runscript
SCIF_APPENV_hello_world=/scif/apps/hello-world/scif/environment.sh
SCIF_APPRUN_hello_world=/scif/apps/hello-world/scif/runscript
SCIF_APPLABELS_hello_world=/scif/apps/hello-world/scif/labels.json
SCIF_APPHELP=/scif/apps/hello-world/scif/runscript.help
SCIF_APPLIB_hello_world=/scif/apps/hello-world/lib
SCIF_APPS=/scif/apps
SCIF_APPMETA_hello_world=/scif/apps/hello-world/scif
SCIF_APPNAME_hello_world=hello-world
SCIF_APPBIN_hello_world=/scif/apps/hello-world/bin
SCIF_APPLIB=/scif/apps/hello-world/lib
SCIF_APPRECIPE=/scif/apps/hello-world/scif/hello-world.scif
SCIF_MESSAGELEVEL=INFO
SCIF_APPBIN=/scif/apps/hello-world/bin
SCIF_APPNAME=hello-world
SCIF_APPROOT_hello_world=/scif/apps/hello-world
Start an interactive python shell to interact with the python client
docker run -it vanessa/hello-world-scif pyshell
Found configurations for 1 scif apps
hello-world
[scif] /scif hello-world
Python 3.6.3 |Anaconda, Inc.| (default, Oct 13 2017, 12:02:49)
Type 'copyright', 'credits' or 'license' for more information
IPython 6.1.0 -- An enhanced Interactive Python. Type '?' for help.
In [1]:
That's it for Docker! Next we review Singularity. Or just see the commands side by side.
Again, first build your container!
sudo singularity build hello-world Singularity
If you don't know anything, you might execute the container. And then you discover the scif entrypoint to guide you!
./hello-world
Scientific Filesystem [v0.0.4]
usage: scif [-h] [--debug] [--quiet] [--writable]
{version,pyshell,shell,preview,help,install,inspect,run,apps,dump,exec}
...
scientific filesystem tools
optional arguments:
-h, --help show this help message and exit
--debug use verbose logging to debug.
--quiet suppress print output
--writable, -w for relevant commands, if writable SCIF is needed
actions:
actions for Scientific Filesystem
{version,pyshell,shell,preview,help,install,inspect,run,apps,dump,exec}
scif actions
version show software version
pyshell Interactive python shell to scientific filesystem
shell shell to interact with scientific filesystem
preview preview changes to a filesytem
help look at help for an app, if it exists.
install install a recipe on the filesystem
inspect inspect an attribute for a scif installation
run entrypoint to run a scientific filesystem
apps list apps installed
dump dump recipe
exec execute a command to a scientific filesystem
List apps
./hello-world apps
SCIF [app] [root]
1 hello-world /scif/apps/hello-world
Get help for hello world
./hello-world help hello-world
This is an example "Hello World" application. You can install it to a
Scientific Filesystem (scif) with the command:
scif install hello-world.scif
if you need to install scif:
pip install scif
Run "hello-world"
./hello-world run hello-world
[hello-world] executing /bin/bash /scif/apps/hello-world/scif/runscript
Hello World!
Execute a command in context of the app "hello world." Notice how we replace the typical $ for the environment variable with [e]
./hello-world exec hello-world ls [e]SCIF_APPROOT
[hello-world] executing /bin/ls $SCIF_APPROOT
bin
lib
scif
Inspect the hello-world app
./hello-world inspect hello-world
{
"hello-world": {
"apprun": [
"/bin/bash hello-world.sh"
],
"appinstall": [
"echo \"echo 'Hello World!'\" >> $SCIF_APPBIN/hello-world.sh",
"chmod u+x $SCIF_APPBIN/hello-world.sh"
],
"appenv": [
"THEBESTAPP=$SCIF_APPNAME",
"export THEBESTAPP"
],
"applabels": [
"MAINTAINER Vanessasaur",
"VERSION 1.0"
],
"apphelp": [
"This is an example \"Hello World\" application. You can install it to a",
"Scientific Filesystem (scif) with the command:",
"scif install hello-world.scif",
"if you need to install scif:",
"pip install scif"
]
}
}
Interactively shell into the container in context of the app "hello-world"
./hello-world shell hello-world
[hello-world] executing /bin/bash
vanessa@vanessa-ThinkPad-T460s:/scif/apps/hello-world$ env | grep SCIF_
SCIF_APPMETA=/scif/apps/hello-world/scif
SCIF_DATA=/scif/data
SCIF_APPHELP_hello_world=/scif/apps/hello-world/scif/runscript.help
SCIF_APPDATA=/scif/data/hello-world
THEBESTAPP=$SCIF_APPNAME
SCIF_APPENV=/scif/apps/hello-world/scif/environment.sh
SCIF_APPROOT=/scif/apps/hello-world
SCIF_APPRECIPE_hello_world=/scif/apps/hello-world/scif/hello-world.scif
SCIF_APPDATA_hello_world=/scif/data/hello-world
SCIF_APPLABELS=/scif/apps/hello-world/scif/labels.json
SCIF_APPRUN=/scif/apps/hello-world/scif/runscript
SCIF_APPENV_hello_world=/scif/apps/hello-world/scif/environment.sh
SCIF_APPRUN_hello_world=/scif/apps/hello-world/scif/runscript
SCIF_APPLABELS_hello_world=/scif/apps/hello-world/scif/labels.json
SCIF_APPHELP=/scif/apps/hello-world/scif/runscript.help
SCIF_APPLIB_hello_world=/scif/apps/hello-world/lib
SCIF_APPS=/scif/apps
SCIF_APPMETA_hello_world=/scif/apps/hello-world/scif
SCIF_APPNAME_hello_world=hello-world
SCIF_APPBIN_hello_world=/scif/apps/hello-world/bin
SCIF_APPLIB=/scif/apps/hello-world/lib
SCIF_APPRECIPE=/scif/apps/hello-world/scif/hello-world.scif
SCIF_MESSAGELEVEL=INFO
SCIF_APPBIN=/scif/apps/hello-world/bin
SCIF_APPNAME=hello-world
SCIF_APPROOT_hello_world=/scif/apps/hello-world
Start an interactive python shell to interact with the python client
./hello-world pyshell
Found configurations for 1 scif apps
hello-world
[scif] /scif hello-world
Python 3.6.2 |Anaconda, Inc.| (default, Sep 22 2017, 02:03:08)
[GCC 7.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
(InteractiveConsole)
>>>