From a84e7f21f0ea479054c761d500e6a90fde9ee498 Mon Sep 17 00:00:00 2001
From: Donald Buczek <buczek@molgen.mpg.de>
Date: Thu, 1 Jul 2021 16:30:34 +0200
Subject: [PATCH 01/16] Add vmcontrol.pl

Import existing script vmcontrol.pl to repository and install it into
/usr/bin.

The script currently lives in ~vmprj/bin and is used by multiple
projects. we don't want to have a nfs dependency for this script, so
just install it into the system.

After the planned move of ~vmprj into /var, ~vmprj/bin wouldn't no
longer be a good place for scripts, too.
---
 install.sh             |   1 +
 vmcontrol/vmcontrol.pl | 164 +++++++++++++++++++++++++++++++++++++++++
 2 files changed, 165 insertions(+)
 create mode 100755 vmcontrol/vmcontrol.pl

diff --git a/install.sh b/install.sh
index 70c85ba..4668108 100755
--- a/install.sh
+++ b/install.sh
@@ -222,6 +222,7 @@ install_data mxshadow/mxshadow.cert.pem                   "$DESTDIR$sysconfdir/m
 install_data mxshadow/mxshadow.conf                       "$DESTDIR$sysconfdir/mxshadow.conf"
 install_data mxshadow/mxshadow.service                    "$DESTDIR$systemdunitdir/mxshadow.service"
 install_data misc_etc_files/nsswitch.conf                 "$DESTDIR$sysconfdir/nsswitch.conf"
+install_exec vmcontrol/vmcontrol.pl                       "$DESTDIR$usr_bindir/vmcontrol.pl"
 
 postinstall
 exit
diff --git a/vmcontrol/vmcontrol.pl b/vmcontrol/vmcontrol.pl
new file mode 100755
index 0000000..1427d9c
--- /dev/null
+++ b/vmcontrol/vmcontrol.pl
@@ -0,0 +1,164 @@
+#! /usr/bin/prun perl perl
+use strict;
+use warnings;
+use IO::Socket::UNIX;
+use JSON;
+use Data::Dumper;
+
+our $DEBUG=0;
+
+our $s;
+our $json;
+
+sub read_json() {
+	my $buffer='';
+	while (1) {
+		my $obj=$json->incr_parse($buffer);
+		$DEBUG and defined $obj and print Data::Dumper->Dump([$obj],['RX']);
+		defined $obj and return $obj;
+		my $sts=sysread $s,$buffer,1024;
+		$sts==0 and die "qmp.socket: hangup\n";
+		defined $sts or die "qmp.socket: $!\”";
+	}
+}
+sub write_json {
+	my ($obj)=@_;
+	$DEBUG and print Data::Dumper->Dump([$obj],['TX']);
+	$s->print(encode_json($obj));
+}
+
+sub exec_cmd {
+	my ($command,@args)=@_;
+	write_json({'execute'=>$command,'arguments'=>{@args}});
+	while(1) {
+		my $obj=read_json();
+		$obj->{'return'} and return $obj->{'return'};
+	}
+}
+
+our $PATTERN=qr/^(.+)\.(\d\d\d)\.disk$/;
+our %DISK;       # ( 'github_root' => [ 'ide-hd0',21 ]
+
+sub verify_disks {
+	my ($obj)=@_;
+	for my $dev (@$obj) {
+		my $inserted=$dev->{'inserted'} or next;
+		my $device=$dev->{'device'};
+		$device =~ /^ide\d+-cd\d+$/ and next;
+		my $image=$inserted->{'image'};
+		my $filename=$image->{'filename'};
+		#printf "verify %-20s %s\n",$device,$filename;
+		my ($basename,$nnn)=$filename=~$PATTERN or die "$filename: wrong pattern (expected: NAME.\\d\\d\\d.disk)\n";
+		-s "$basename.disk" or die "$basename.disk: symlink is missing\n";
+		readlink("$basename.disk") eq $filename or die "symlink $basename.disk not pointing to $filename\n";
+
+		my %FILES;
+		opendir my $d,".";
+		while (readdir $d) {
+			my ($cmp_basename,$cmp_nnn)= $_=~$PATTERN or next;
+			$cmp_basename eq $basename or next;
+			$FILES{$_}=1;
+		}
+		delete $FILES{$filename};
+
+
+		my $depth=0;
+		for (my $backing_image=$image->{'backing-image'};$backing_image;$backing_image=$backing_image->{'backing-image'}) {
+			$depth++;
+			my $b_filename=$backing_image->{'filename'};
+			#printf "       %-20s %s\n",'',$b_filename;
+			my ($b_basename,$b_nnn)=$b_filename=~$PATTERN or die "backing file $filename: wrong pattern\n";
+			$b_basename eq $basename or die "$b_filename: wrong basename\n";
+			$b_nnn == $nnn-$depth or die "$b_filename: number should be ".($nnn-$depth)."\n";
+			delete $FILES{$b_filename};
+		}
+		if (%FILES) {
+			warn "unused files: ".join(' ',keys %FILES)."\n";
+		}
+		$DISK{$basename}=[$device,$nnn];
+	}
+}
+
+sub  verify_no_block_jobs_running {
+	my $obj=exec_cmd('query-block-jobs');
+	@$obj and die "block jobs running!\n";
+}
+
+sub wait_block_jobs {
+	while (1) {
+		my $obj=exec_cmd('query-block-jobs');
+		Data::Dumper->Dump([$obj],['O']);
+		@$obj or return;
+		for my $job (@$obj) {
+			my $device=$job->{'device'};
+			my $offset=$job->{'offset'};
+			my $len=$job->{'len'};
+			printf "%-15s %d/%d (%5.1f%%)\n",$device,$offset,$len,$offset*100/$len;
+		}
+		sleep 1;
+	}
+}
+
+sub snapshot {
+	my ($basename)=@_;
+	exists $DISK{$basename} or die "$basename does not exist in VM\n";
+	my ($devname,$nnn)=@{$DISK{$basename}};
+	my $filename=sprintf '%s.%03d.disk',$basename,$nnn+1;
+
+	print "snapshot $devname -> $filename\n";
+	exec_cmd('blockdev-snapshot-sync','device'=>$devname,'snapshot-file'=>$filename);
+	-s "$basename.disk" and unlink "$basename.disk";
+	symlink($filename,"$basename.disk") or die "failed to symlink $basename.disk -> $filename: $!\n";
+	$DISK{$basename}=[$devname,$nnn+1];
+}
+
+sub block_stream {
+	my ($basename)=@_;
+	exists $DISK{$basename} or die "$basename does not exist in VM\n";
+	my ($devname,$nnn)=@{$DISK{$basename}};
+	exec_cmd('block-stream','device'=>$devname);
+}
+
+
+$json=new JSON;
+$s=new IO::Socket::UNIX(Type=>SOCK_STREAM,Peer=>'./qmp.socket') or die "qmp.socket: $!\n";
+exec_cmd('qmp_capabilities');
+
+
+sub USAGE {
+	<<"EOF";
+usage: $0 cmd
+   snapshot NAME     # new instance NAME.xxx.disk
+   block-stream NAME # start stream up to top layer 
+     ( hint: `fstrim -av` on the vm may save some space )
+   wait              # wait till all block jobs are finished
+   powerdown         # send ACPI powerdown
+   noop              # do nothing, but verify disks as always
+EOF
+}
+
+@ARGV or die USAGE;
+my ($cmd,@args)=(@ARGV);
+
+my $block_info=exec_cmd('query-block');
+verify_disks($block_info);
+
+if ($cmd eq 'snapshot') {
+	@args==1 or die USAGE;
+	verify_no_block_jobs_running();
+	snapshot(@args);
+} elsif ($cmd eq 'block-stream') {
+	@args==1 or die USAGE;
+	verify_no_block_jobs_running();
+	block_stream(@args);
+} elsif ($cmd eq 'wait') {
+	@args==0 or die USAGE;
+	wait_block_jobs();
+} elsif ($cmd eq 'powerdown') {
+	@args==0 or die USAGE;
+	exec_cmd('system_powerdown');
+} elsif ($cmd eq 'noop') {
+	@args==0 or die USAGE;
+} else {
+	die USAGE;
+}

From 1eb2502998b0a585481ef89f1512f3e1ec7ca231 Mon Sep 17 00:00:00 2001
From: thomas <kreitler@molgen.mpg.de>
Date: Tue, 6 Jul 2021 19:04:15 +0200
Subject: [PATCH 02/16] usrlocalpkg: add binary rstudio package for debian

Use for comparison and bug hunting.

Introducing also a more or less smart launcher
for the case, when the workstation uses the nvidia
driver and the remote doesn't. It is called rstudio-nv.
---
 usrlocalpkg/admin/config | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/usrlocalpkg/admin/config b/usrlocalpkg/admin/config
index 441311a..6798a30 100644
--- a/usrlocalpkg/admin/config
+++ b/usrlocalpkg/admin/config
@@ -1411,6 +1411,9 @@ rstudio-1.4.1103-0
 	rstudio
 	rsession
 
+rstudio-debpkg-1.4.1717-0
+  rstudio-debpkg=rstudio
+  rstudio-debpkg-nv=rstudio-nv
 
 R-devel=R-devel-2017-02-02-1
 

From 0975c41784bafe4c274c6f30510ce15999216b0b Mon Sep 17 00:00:00 2001
From: Donald Buczek <buczek@molgen.mpg.de>
Date: Tue, 27 Jul 2021 13:36:34 +0200
Subject: [PATCH 03/16] usrlocalpkg: Update rust default to 1.52.1

---
 usrlocalpkg/admin/config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/usrlocalpkg/admin/config b/usrlocalpkg/admin/config
index 6798a30..e27bf8b 100644
--- a/usrlocalpkg/admin/config
+++ b/usrlocalpkg/admin/config
@@ -1515,7 +1515,7 @@ CellProfiler-2.2.0-0
 CellProfiler-3.1.5-0
   cellprofiler
 
-rustc-1.50.0-0
+rustc-1.52.1-0
   rustc
   cargo
   cbindgens

From 77b1fb2f53382ccea9a9c1a153830510b581ade9 Mon Sep 17 00:00:00 2001
From: Donald Buczek <buczek@molgen.mpg.de>
Date: Thu, 29 Jul 2021 09:25:09 +0200
Subject: [PATCH 04/16] usrlocalpkg: Add alias and more wrapper for rust

Add package alias "rust" so that we can easily run tools from the
current rust package which don't deserve a wrapper on their own.

For example

    prun rust miri

Add wrappers for `rustdoc` and `rustfmt`. These are available via cargo,
too, ( `cargo doc`, `cargo fmt` ) but, for example, `cargo help fmt`
refers to "Options passed to rustfmt" so it would be useful, if
`rustfmt --help` would work. Also, external documentation might suggest
users to run these commands directly.
---
 usrlocalpkg/admin/config | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/usrlocalpkg/admin/config b/usrlocalpkg/admin/config
index e27bf8b..6f92311 100644
--- a/usrlocalpkg/admin/config
+++ b/usrlocalpkg/admin/config
@@ -1515,10 +1515,12 @@ CellProfiler-2.2.0-0
 CellProfiler-3.1.5-0
   cellprofiler
 
-rustc-1.52.1-0
+rust=rustc-1.52.1-0
   rustc
   cargo
   cbindgens
+  rustdoc
+  rustfmt
 
 apache-maven-3.6.0-0
   mvn mvnDebug

From 9ce80222f0060bc922942d0f2a12a094c17a4a85 Mon Sep 17 00:00:00 2001
From: thomas <kreitler@molgen.mpg.de>
Date: Thu, 29 Jul 2021 13:25:05 +0200
Subject: [PATCH 05/16] usrlocalpkg: cuda, update shortcuts

Well, looks like they aren't used that much.
---
 usrlocalpkg/admin/config | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/usrlocalpkg/admin/config b/usrlocalpkg/admin/config
index 6f92311..3218d8c 100644
--- a/usrlocalpkg/admin/config
+++ b/usrlocalpkg/admin/config
@@ -1426,13 +1426,18 @@ chromium=chromium-89.0.4389.128-0
 
 cuda-9.0=cuda-9.0.176-0
 cuda-9.1=cuda-9.1.85-0
+cuda-9.2=cuda-9.2.148-0
 cuda-9=cuda-9.0          # keep default 9.0 because of tensorflow
 
 cuda-10.0=cuda-10.0.130-0
 cuda-10.1=cuda-10.1.105-0
-cuda-10.2=cuda-10.2.89-0
+cuda-10.2=cuda-10.2.89-1
 cuda-10=cuda-10.0        # keep default 10.0 because of tensorflow ...
 
+cuda-11.0=cuda-11.0.3-0
+cuda-11.1=ccuda-11.1.1-0
+cuda-11.3=ccuda-11.3.1-0
+
 gcc-5=gcc-5.5.0-1
   ecj
   gappletviewer

From 8e5202ec21b2e91099b6b1e9bc4a85656003c4af Mon Sep 17 00:00:00 2001
From: thomas <kreitler@molgen.mpg.de>
Date: Thu, 29 Jul 2021 13:26:17 +0200
Subject: [PATCH 06/16] usrlocalpkg: switch to bazel-4.1.0

---
 usrlocalpkg/admin/config | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/usrlocalpkg/admin/config b/usrlocalpkg/admin/config
index 3218d8c..674b420 100644
--- a/usrlocalpkg/admin/config
+++ b/usrlocalpkg/admin/config
@@ -1627,6 +1627,9 @@ bazel-0.28.1-0
   bazel-0.28=bazel
 
 bazel=bazel-3.4.1-0
+  bazel-3.4.1=bazel
+
+bazel=bazel-4.1.0-0
   bazel
 
 

From 0f121b7bf92a28d405fd38b68f94da2738f9b8a2 Mon Sep 17 00:00:00 2001
From: thomas <kreitler@molgen.mpg.de>
Date: Thu, 29 Jul 2021 13:31:13 +0200
Subject: [PATCH 07/16] usrlocalpkg: fix typos in config

OMG (I sould keep my door closed!)
---
 usrlocalpkg/admin/config | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/usrlocalpkg/admin/config b/usrlocalpkg/admin/config
index 674b420..d6d20cc 100644
--- a/usrlocalpkg/admin/config
+++ b/usrlocalpkg/admin/config
@@ -1435,8 +1435,8 @@ cuda-10.2=cuda-10.2.89-1
 cuda-10=cuda-10.0        # keep default 10.0 because of tensorflow ...
 
 cuda-11.0=cuda-11.0.3-0
-cuda-11.1=ccuda-11.1.1-0
-cuda-11.3=ccuda-11.3.1-0
+cuda-11.1=cuda-11.1.1-0
+cuda-11.3=cuda-11.3.1-0
 
 gcc-5=gcc-5.5.0-1
   ecj
@@ -1626,7 +1626,7 @@ voreen
 bazel-0.28.1-0
   bazel-0.28=bazel
 
-bazel=bazel-3.4.1-0
+bazel-3.4.1-0
   bazel-3.4.1=bazel
 
 bazel=bazel-4.1.0-0

From e9c18017f511666907bb8155dacc2dc201f323a7 Mon Sep 17 00:00:00 2001
From: Paul Menzel <pmenzel@molgen.mpg.de>
Date: Mon, 2 Aug 2021 15:16:22 +0200
Subject: [PATCH 08/16] systemd/enable_overcommit_memory: Use `/sbin/sysctl`
 for Ubuntu
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Ubuntu’s package *procps* 2:3.3.16-5ubuntu3.1 installs `sysctl` only in
`/sbin/sysctl`, and therefore the service unit fails to be started.

Instead of `/usr/sbin/sysctl`, use `/sbin/sysctl`, which is a symbolic
link on MarIuX.

    $ ls -l /sbin/sysctl # usrlinks-1.0-0.x86_64
    lrwxrwxrwx 1 root root 16 May 29 15:02 /sbin/sysctl -> /usr/sbin/sysctl

Alternatively, as systemd does not require absolute pathnames anymore,
only `sysctl` could be used, but be explicit for now.
---
 misc_systemd_units/enable_overcommit_memory.service | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/misc_systemd_units/enable_overcommit_memory.service b/misc_systemd_units/enable_overcommit_memory.service
index 678c68e..302248f 100644
--- a/misc_systemd_units/enable_overcommit_memory.service
+++ b/misc_systemd_units/enable_overcommit_memory.service
@@ -8,8 +8,8 @@ ConditionHost=|flughafenberlinbrandenburgwillybrandt.molgen.mpg.de
 [Service]
 Type=oneshot
 RemainAfterExit=yes
-ExecStart=/usr/sbin/sysctl vm.overcommit_memory=0
-ExecStop=/usr/sbin/sysctl vm.overcommit_memory=2
+ExecStart=/sbin/sysctl vm.overcommit_memory=0
+ExecStop=/sbin/sysctl vm.overcommit_memory=2
 
 [Install]
 WantedBy=graphical.target

From dac25ac73596058534acc0cb2987375e776d41a6 Mon Sep 17 00:00:00 2001
From: thomas <kreitler@molgen.mpg.de>
Date: Fri, 6 Aug 2021 17:43:47 +0200
Subject: [PATCH 09/16] usrlocalpkg: Add python3.9 and CellProfiler-4

Just provide python3.9, and check a little bit before making it the
default.
---
 usrlocalpkg/admin/config | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/usrlocalpkg/admin/config b/usrlocalpkg/admin/config
index d6d20cc..1b6e94c 100644
--- a/usrlocalpkg/admin/config
+++ b/usrlocalpkg/admin/config
@@ -1352,6 +1352,14 @@ python-3.8=python-3.8.9-1
 
 python3.8=python-3.8
 
+python-3.9=python-3.9.6-0
+	python3.9
+	python3.9-config
+	pip3.9
+	pydoc3.9
+
+python3.9=python-3.9
+
 # b) default python, see PEP 0394 too
 
 python-3=python-3.8
@@ -1520,6 +1528,9 @@ CellProfiler-2.2.0-0
 CellProfiler-3.1.5-0
   cellprofiler
 
+CellProfiler-4.2.1-0
+  cellprofiler4=cellprofiler
+
 rust=rustc-1.52.1-0
   rustc
   cargo

From 7572632d335efe3b702dbebb686a6929badfebc7 Mon Sep 17 00:00:00 2001
From: thomas <kreitler@molgen.mpg.de>
Date: Fri, 6 Aug 2021 18:04:39 +0200
Subject: [PATCH 10/16] mxsnoop: Add prototype

Use to monitor network traffic on site.
---
 mxsnoop/mxsnoop.sh | 117 +++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 117 insertions(+)
 create mode 100755 mxsnoop/mxsnoop.sh

diff --git a/mxsnoop/mxsnoop.sh b/mxsnoop/mxsnoop.sh
new file mode 100755
index 0000000..a8d39a7
--- /dev/null
+++ b/mxsnoop/mxsnoop.sh
@@ -0,0 +1,117 @@
+#!/bin/bash
+
+#
+#  +--------------+   (!)   +----------------------+        +---****
+#  |              |         |        br01          |        |
+#  | THE SUSPECT  O]===X===[O   SCHNUEFFELSTUECK   O]======[O  WIS-NET
+#  |              |         |INLET           OUTLET|        |
+#  +--------------+         +----------------------+        +---****
+#                                        (MX_NETDEV)
+
+#  Basics: https://wiki.archlinux.org/title/Network_bridge
+
+# GATEWAY=10.0.3.1
+# BROADCAST=10.0.3.255
+# NETMASK=255.255.255.0
+# NIDL=24
+
+GATEWAY=141.14.16.128
+BROADCAST=141.14.31.255
+NETMASK=255.255.240.0
+NIDL=20
+
+INLET=${INLET:-}
+OUTLET=${OUTLET:-}
+BRIDGE=br01
+
+TRANSPARENT=${TRANSPARENT:-}
+STP=${STP:-}
+
+function die() { echo $1; exit 1; }
+
+type ip > /dev/null || \
+  die 'Error: Tools not available, check for ip command.'
+
+MXHOSTCONF=${MXHOSTCONF:-/etc/local/mxhost.conf}
+source $MXHOSTCONF || die "# Error: No 'mxhost.conf' ?"
+test -n "$MX_IPADDR" || die '# Error: MX_IPADDR missing.'
+
+if [ -z "$OUTLET" ]; then
+  test -n "$MX_NETDEV" || die '# Error: MX_NETDEV missing?'
+  test -e /sys/class/net/$MX_NETDEV || die "# Error: $MX_NETDEV missing."
+  OUTLET=$MX_NETDEV
+fi
+
+
+# inlet was present at boot time -> netXY, or plugged later -> Search for ethX
+if [ -z "$INLET" ]; then # find the (sole) inlet
+  for D in net{00..09} eth{0..9}; do
+    test -e /sys/class/net/$D || continue
+    test $D = $OUTLET && continue
+    test -n "$INLET" && \
+      die 'Error: Too many network devices (netXY) present, use INLET=dev (OUTLET=dev ?).'
+    INLET=$D
+  done
+fi
+
+test -z "$INLET" && die '# Error: no second network device found.'
+
+echo "# Note: about to setup/destroy $BRIDGE between $INLET (INLET) and $OUTLET (OUTLET), IP: $MX_IPADDR"
+
+cmd="$1"
+
+case "$cmd" in
+
+  start)
+
+    if [ -z "$STP" ]; then
+      ip link add dev $BRIDGE type bridge
+    else
+      ip link add dev $BRIDGE type bridge stp_state 1
+    fi
+
+    ip address flush dev $INLET
+    ip address flush dev $OUTLET
+
+    ip link set $INLET master $BRIDGE
+    ip link set $OUTLET master $BRIDGE
+
+    if [ -z "$TRANSPARENT" ] ; then
+      ip addr add $MX_IPADDR/$NIDL broadcast $BROADCAST dev $BRIDGE
+      ip link set up dev $BRIDGE
+      ip route add default via $GATEWAY dev $BRIDGE
+    fi
+
+    ip link set dev $INLET up
+    ip link set dev $OUTLET up
+
+    ;;
+
+  stop)
+
+    ip link set $INLET nomaster
+    ip link set $OUTLET nomaster
+    ip link delete $BRIDGE type bridge
+
+    ip addr add $MX_IPADDR/$NIDL broadcast $BROADCAST dev $OUTLET
+    ip link set dev $OUTLET up
+    ip route add default via $GATEWAY
+
+    ;;
+
+  restart)
+
+    $0 stop
+    sleep 1
+    $0 start
+    ;;
+
+  *)
+
+    echo "#   usage:     [INLET=dev] [OUTLET=dev] $0 [start|stop|restart]"
+    echo "# options:     TRANSPARENT=1 doesn't bind IP on the bridge"
+    echo "#              STP=1 enables Spanning Tree"
+    ;;
+
+esac
+

From e0336eb8139246c42253f40b3d5e43d2020ed262 Mon Sep 17 00:00:00 2001
From: thomas <kreitler@molgen.mpg.de>
Date: Wed, 11 Aug 2021 17:11:18 +0200
Subject: [PATCH 11/16] prun: Add documentation in markdown format

Manual pages can be generated with:

  pandoc --standalone --to man prun.md -o prun.man.1
---
 prun/pman.md  |  37 ++++++++++++++++++
 prun/prun.md  | 102 ++++++++++++++++++++++++++++++++++++++++++++++++++
 prun/ptype.md |  42 +++++++++++++++++++++
 3 files changed, 181 insertions(+)
 create mode 100644 prun/pman.md
 create mode 100644 prun/prun.md
 create mode 100644 prun/ptype.md

diff --git a/prun/pman.md b/prun/pman.md
new file mode 100644
index 0000000..8518d23
--- /dev/null
+++ b/prun/pman.md
@@ -0,0 +1,37 @@
+% PTYPE(1) | Mariux Tools Documentation
+
+NAME
+====
+
+**pman** - view manual pages installed in Mariux packages.
+
+SYNOPSIS
+========
+
+| **pman command**
+
+DESCRIPTION
+===========
+
+**ptype** uses the PATH set in the package wrapper and tries to find a manual page in the package directory.
+
+EXAMPLES
+========
+
+**display manpage found in /pkg/stellarium-0.21.0-0/share/man/man1**
+: pman stellarium
+
+
+BUGS
+====
+
+**pman** is very naive in looking up man pages, so your mileage may vary.
+
+See GitHub Issues: <https://github.molgen.mpg.de/mariux64/mxtools>
+
+SEE ALSO
+========
+
+**prun(1)**, **ptype(1)**, **man(1)**
+
+
diff --git a/prun/prun.md b/prun/prun.md
new file mode 100644
index 0000000..ba36071
--- /dev/null
+++ b/prun/prun.md
@@ -0,0 +1,102 @@
+% PRUN(1) Version n/a | Mariux Tools Documentation
+
+NAME
+====
+
+**prun** - Run Mariux packages (reads 'Package RUN').
+
+SYNOPSIS
+========
+
+| **prun package command** [COMMANDOPTION]...
+
+DESCRIPTION
+===========
+
+Runs applications, scripting languages, compilers, etc., from a dedicated directory.
+
+The main usage is to run software in a specific version, or to provide a given environment. See **EXAMPLES** below.
+
+There are some advantages over so called 'virtual environments' and the like. Packages are immutable, once installed they never change, thereby increasing the chances that an old program/script will also run in a few years. The packages also 
+use a standardized call procedure, independent of personal (un-)settings, thus an existing pipeline may be shared between different users.
+
+The whole 'magic' behind **prun** is, that it transparently sets the PATH variable and possibly LD_LIBRARY_PATH for the actual call without spoiling the default environment.
+
+EXAMPLES
+========
+
+
+**Run R-Studio with a brand new R version**
+
+: prun R-4.1.0-0 rstudio
+
+**Use an ancient python to run an unmaintained script**
+
+: prun python-2.7.13-2 /project/cruft/bin/old_script.py
+
+**Run nvidia nvcc from cuda-11.3 and list supported architectures**
+
+: prun cuda-11.3 nvcc --list-gpu-code
+
+**Start a plain shell with gcc-10.2 in the PATH**
+
+:  prun gcc-10.2.0-0 bash --norc
+
+**Or just show the manual page for gcc-10.2**
+
+:  prun gcc-10.2.0-0 man gcc
+
+**Create an own alias for a scripting language**
+
+: alias myperl='prun perl-5.18.2-0 perl'
+
+**Use prun in a script shebang**
+
+: `#! /usr/bin/prun perl-5.18.2-0 perl`
+
+**Alternatively using source**
+
+:  An alternative way to set a distinct environment is to source the profile from /pkg/FooBar-12.3.
+But beware, such a source command should **never** make it into the **\~/.bashrc** - in the worst case it may inhibit your login!
+(N.b. the alias method mentioned above is safe)
+
+\ 
+: source /pkg/gcc-10.2.0-0/profile
+
+
+FILES
+=====
+
+*/package/FOO* or */pkg/BAR*
+
+:   Mountpoint (top directory) for selected package.
+
+*/package/FOO/profile* or */pkg/BAR/profile*
+
+:   Contains settings for PATH, libraries, and possibly other stuff.
+
+*/usr/local/package/lib/\**
+
+:   Primary wrappers for individual packages.
+
+*/usr/local/package/admin/config*
+
+:   Definition of binaries provided and optional shortcuts.
+
+
+BUGS
+====
+
+See GitHub Issues: <https://github.molgen.mpg.de/mariux64/mxtools>
+
+AUTHORS
+=======
+
+D.Buczek, P.Marquardt, M.Tolzmann
+
+SEE ALSO
+========
+
+**ptype(1)**, **pman(1)**, **bash(1)**, **ld.so(8)**
+
+
diff --git a/prun/ptype.md b/prun/ptype.md
new file mode 100644
index 0000000..72c7d74
--- /dev/null
+++ b/prun/ptype.md
@@ -0,0 +1,42 @@
+% PTYPE(1) | Mariux Tools Documentation
+
+NAME
+====
+
+**ptype** - small **type** like tool for Mariux packages.
+
+SYNOPSIS
+========
+
+| **ptype command**
+
+DESCRIPTION
+===========
+
+Similar to **type** or **which**. **ptype** gives information about a package binary. **type** would only tell something about the package wrapper, and not about the package where the real program is. 
+
+```
+
+  #> type snakemake
+  snakemake is /usr/local/package/bin/snakemake
+
+  #> ptype snakemake
+  snakemake is /pkg/python-3.8.9-1/bin/snakemake  ...
+               ... (/usr/local/package/lib/python.profile)
+
+
+```
+
+BUGS
+====
+
+**ptype** only handles true wrapper scripts from /usr/local/package/bin, not the aliases. I.e. **ptype R** works, **ptype R4** not.
+
+See GitHub Issues: <https://github.molgen.mpg.de/mariux64/mxtools>
+
+SEE ALSO
+========
+
+**prun(1)**, **pman(1)**
+
+

From d841b64c7b2b7c3c2416406e17ca468063e08f59 Mon Sep 17 00:00:00 2001
From: Donald Buczek <buczek@molgen.mpg.de>
Date: Thu, 12 Aug 2021 10:39:06 +0200
Subject: [PATCH 12/16] Add build/install logic for prun manpages

---
 .gitignore |  1 +
 Makefile   | 16 +++++++++++-----
 install.sh |  4 ++++
 3 files changed, 16 insertions(+), 5 deletions(-)

diff --git a/.gitignore b/.gitignore
index 2f683ef..41c83a2 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1 +1,2 @@
 setuid/setuid
+prun/*.1
diff --git a/Makefile b/Makefile
index 9810ebc..481b18e 100644
--- a/Makefile
+++ b/Makefile
@@ -64,13 +64,18 @@ INSTALL=install -v
 INSTALL_PROGRAM = $(INSTALL)
 INSTALL_DATA = $(INSTALL) -m 644
 
-all:
-	@echo 'Nothing to be done. Ready for "make install"'
+manpages += prun/prun.1 prun/pman.1 prun/ptype.1
 
-install:
+all: $(manpages)
+
+clean:
+	@rm $(manpages)
+
+install: all
 	@prefix="$(prefix)" usr_prefix="$(usr_prefix)" usrlocal_prefix="$(usrlocal_prefix)" \
 	root_exec_prefix="$(root_exec_prefix)"         root_bindir="$(root_bindir)"    root_sbindir="$(root_sbindir)" \
 	usr_exec_prefix="$(usr_exec_prefix)"           usr_bindir="$(usr_bindir)"      usr_sbindir="$(usr_sbindir)" \
+	usr_mandir="$(usr_mandir)" \
 	usrlocal_exec_prefix="$(usrlocal_exec_prefix)" usrlocal_bindir="$(usrlocal_bindir)" usrlocal_sbindir="$(usrlocal_sbindir)" \
 	sysconfdir="$(sysconfdir)"                     systemdunitdir="$(systemdunitdir)" \
 	udev_rulesdir="$(udev_rulesdir)"               udev_helperdir="$(udev_helperdir)" \
@@ -79,6 +84,7 @@ install:
 	DESTDIR="$(DESTDIR)" \
 	./install.sh
 
-.PHONY: all install
-
+.PHONY: all install clean
 
+%.1: %.md
+	pandoc --standalone --to man $< -o $@
diff --git a/install.sh b/install.sh
index 4668108..385614b 100755
--- a/install.sh
+++ b/install.sh
@@ -21,6 +21,7 @@ fi
 : ${usr_exec_prefix:=$usr_prefix}
 : ${usr_bindir:=$usr_exec_prefix/bin}
 : ${usr_sbindir:=$usr_exec_prefix/sbin}
+: ${usr_mandir:=$usr_exec_prefix/man}
 
 : ${usrlocal_exec_prefix:=$usrlocal_prefix}
 : ${usrlocal_bindir:=$usrlocal_exec_prefix/bin}
@@ -223,6 +224,9 @@ install_data mxshadow/mxshadow.conf                       "$DESTDIR$sysconfdir/m
 install_data mxshadow/mxshadow.service                    "$DESTDIR$systemdunitdir/mxshadow.service"
 install_data misc_etc_files/nsswitch.conf                 "$DESTDIR$sysconfdir/nsswitch.conf"
 install_exec vmcontrol/vmcontrol.pl                       "$DESTDIR$usr_bindir/vmcontrol.pl"
+install_data prun/prun.1                                  "$DESTDIR$usr_mandir/man1/prun.1"
+install_data prun/ptype.1                                 "$DESTDIR$usr_mandir/man1/ptype.1"
+install_data prun/pman.1                                  "$DESTDIR$usr_mandir/man1/pman.1"
 
 postinstall
 exit

From fad0b5454a6d4788d9133a348e7039197b22316b Mon Sep 17 00:00:00 2001
From: Donald Buczek <buczek@molgen.mpg.de>
Date: Thu, 12 Aug 2021 12:11:38 +0200
Subject: [PATCH 13/16] Makefile: Shut up "make clean"

Use `-f` flag of `rm` to avoid error messages from `make clean` when the
targets files don't exist.
---
 Makefile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Makefile b/Makefile
index 481b18e..164c794 100644
--- a/Makefile
+++ b/Makefile
@@ -69,7 +69,7 @@ manpages += prun/prun.1 prun/pman.1 prun/ptype.1
 all: $(manpages)
 
 clean:
-	@rm $(manpages)
+	@rm -f $(manpages)
 
 install: all
 	@prefix="$(prefix)" usr_prefix="$(usr_prefix)" usrlocal_prefix="$(usrlocal_prefix)" \

From d7d563834ade87882828968acde738307ef06f5a Mon Sep 17 00:00:00 2001
From: Donald Buczek <buczek@molgen.mpg.de>
Date: Thu, 12 Aug 2021 12:14:04 +0200
Subject: [PATCH 14/16] Makefile: Avoid running "pandoc" as root

---
 Makefile | 1 +
 1 file changed, 1 insertion(+)

diff --git a/Makefile b/Makefile
index 164c794..e984744 100644
--- a/Makefile
+++ b/Makefile
@@ -87,4 +87,5 @@ install: all
 .PHONY: all install clean
 
 %.1: %.md
+	@if [ "$$UID" = 0 ]; then echo "Please build (\`make\`) as non-root before running \`make install\` as root" >&2;exit 1;fi
 	pandoc --standalone --to man $< -o $@

From 52b24e5857ac9bb7cd14b4db2f7e830843e1a504 Mon Sep 17 00:00:00 2001
From: thomas <kreitler@molgen.mpg.de>
Date: Mon, 16 Aug 2021 13:49:47 +0200
Subject: [PATCH 15/16] prun man pages: cleanup

Remove authors from prun.md, reformat
Remove copy-and-paste errors in pman.md
---
 prun/pman.md | 4 ++--
 prun/prun.md | 8 +-------
 2 files changed, 3 insertions(+), 9 deletions(-)

diff --git a/prun/pman.md b/prun/pman.md
index 8518d23..ae747a8 100644
--- a/prun/pman.md
+++ b/prun/pman.md
@@ -1,4 +1,4 @@
-% PTYPE(1) | Mariux Tools Documentation
+% PMAN(1) | Mariux Tools Documentation
 
 NAME
 ====
@@ -13,7 +13,7 @@ SYNOPSIS
 DESCRIPTION
 ===========
 
-**ptype** uses the PATH set in the package wrapper and tries to find a manual page in the package directory.
+**pman** uses the PATH set in the package wrapper and tries to find a manual page in the package directory.
 
 EXAMPLES
 ========
diff --git a/prun/prun.md b/prun/prun.md
index ba36071..b9cc124 100644
--- a/prun/prun.md
+++ b/prun/prun.md
@@ -17,8 +17,7 @@ Runs applications, scripting languages, compilers, etc., from a dedicated direct
 
 The main usage is to run software in a specific version, or to provide a given environment. See **EXAMPLES** below.
 
-There are some advantages over so called 'virtual environments' and the like. Packages are immutable, once installed they never change, thereby increasing the chances that an old program/script will also run in a few years. The packages also 
-use a standardized call procedure, independent of personal (un-)settings, thus an existing pipeline may be shared between different users.
+There are some advantages over so called 'virtual environments' and the like. Packages are immutable, once installed they never change, thereby increasing the chances that an old program/script will also run in a few years. The packages also use a standardized call procedure, independent of personal (un-)settings, thus an existing pipeline may be shared between different users.
 
 The whole 'magic' behind **prun** is, that it transparently sets the PATH variable and possibly LD_LIBRARY_PATH for the actual call without spoiling the default environment.
 
@@ -89,11 +88,6 @@ BUGS
 
 See GitHub Issues: <https://github.molgen.mpg.de/mariux64/mxtools>
 
-AUTHORS
-=======
-
-D.Buczek, P.Marquardt, M.Tolzmann
-
 SEE ALSO
 ========
 

From 78ff0435334c2b8ca5db1f8863a03c9f2d68bdd4 Mon Sep 17 00:00:00 2001
From: thomas <kreitler@molgen.mpg.de>
Date: Mon, 16 Aug 2021 14:59:43 +0200
Subject: [PATCH 16/16] usrlocalpkg: switch to python-3.9

Summary:

 - meson version is now 0.59.0
 - snakemake is 6.6.1
 - pdbfixer is used by AlphaFold, so it is in the path.
---
 usrlocalpkg/admin/config | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/usrlocalpkg/admin/config b/usrlocalpkg/admin/config
index 1b6e94c..268d4ef 100644
--- a/usrlocalpkg/admin/config
+++ b/usrlocalpkg/admin/config
@@ -1362,7 +1362,7 @@ python3.9=python-3.9
 
 # b) default python, see PEP 0394 too
 
-python-3=python-3.8
+python-3=python-3.9
 	python3
 	python3-config
 	idle3=idle
@@ -1373,7 +1373,7 @@ python-3=python-3.8
 python3=python-3
 
 # c) manage python based tools (meson, snakemake, ...)
-# mind python3-wrapper.be0
+# Check existence! And mind python3-wrapper.be0 too
 
 python=python-3
   bamCompare
@@ -1395,6 +1395,7 @@ python=python-3
   multiqc
   nbshow
   pairtools
+  pdbfixer
   pgt
   pip
   pyGenomeTracks