Add a slurm_init command.

It should allow simplify the documentation for using SLURM, allow for auto-testing the documentation, and having a fixed location to expect the slurm library by default could allow us to auto pick it up if it is available.

Author: jmchilton

planemo/commands/cmd_slurm_init.py

@@ -0,0 +1,35 @@
+"""Module describing the planemo ``slurm_init`` command."""
+import shutil
+import tempfile
+
+import click
+
+from planemo.cli import command_function
+from planemo.io import info, shell, untar_to
+
+SLRUM_DRMAA_VERSION = "1.1.4"
+DOWNLOAD_URL = f"https://github.com/natefoo/slurm-drmaa/releases/download/{SLRUM_DRMAA_VERSION}/slurm-drmaa-{SLRUM_DRMAA_VERSION}.tar.gz"
+
+@click.command("slurm_init")
+@command_function
+def cli(ctx, **kwds):
+    """Initialize a copy of the SLURM DRMAA library."""
+    dest = f"{ctx.workspace}/libdrmaa.so"
+    tempdir = tempfile.mkdtemp()
+    tar_args = ["-zxf", "-", "--strip-components=1"]
+    try:
+        # This used to show the wget command (and in fact use wget), it doesn't anymore but
+        # this should be restored. The point is to show developers what is happening and how to do it.
+        untar_to(DOWNLOAD_URL, tar_args=tar_args, dest_dir=tempdir)
+        shell(["mkdir", "dest"], cwd=tempdir)
+        shell(["./autogen.sh"], cwd=tempdir)
+        shell(["./configure", f"--prefix={tempdir}/dist"], cwd=tempdir)
+        shell(["make"], cwd=tempdir)
+        shell(["make install"], cwd=tempdir)
+        shutil.move(
+            f"{tempdir}/dist/lib/libdrmaa.so",
+            dest
+        )
+        info(f"SLURM DRMAA library initialized successfully and copied to {dest}.")
+    finally:
+        shutil.rmtree(tempdir)