March 10, 2013

The FPC (FingerPrinted Contigs) program,
home page http://www.agcol.arizona.edu/software/fpc/
produced the following error on Fedora 15

FATAL ERROR (ruid: null, euid: null, nodeid: null, program: null, version: null, file: graphgdk.c, line: 194) - Can't load default font 8x13

Google results found the problem but no solution. Here it is, based on a post from 2005

1. How do I see what fonts are installed?
   

   $ xlsfonts | less
   ...
   -urw-urw palladio l-medium-r-normal--0-0-0-0-p-0-koi8-uni
   6x13
   cursor
   fixed
   lucidasans-10
   ...

2. Install the missing font
   

   $ sudo yum install xorg-x11-fonts-misc

3. Check font list again to verify that the 8x13 font was installed
   

   $ xlsfonts | less
   ...
   7x14bold
   8x13
   8x13bold
   8x16
   ...

Earlier reference: http://forums.fedoraforum.org/showthread.php?t=260563

 

Jan. 25, 2013

The 36th International Carrot Conference is coming to Madison, Wisconsin this year.
August 15-16, 2013

The web site is http://www.vcru.wisc.edu/simonlab/carrotconference/index.html

October 30, 2011

Another post in the series of "things that are not on the internet yet", How to install Sequin on Fedora 15, 64-bit

The Sequin home page is http://www.ncbi.nlm.nih.gov/Sequin/download/seq_unix_download.html

Download Sequin, and uncompress it

[user@host programinstallers]$ wget -N ftp://ftp.ncbi.nih.gov/sequin/CURRENT/sequin.linux-x86.tar.gz

Warning, this archive will extract into the current directory

[user@host programinstallers]$ mkdir /usr/local/bin/sequin
[user@host programinstallers]$ cd /usr/local/bin/sequin
[user@host sequin]$ tar -zxvf /programinstallers/sequin.linux-x86.tar.gz

Modify the default PATH so that the program is accessible to all users

[user@host sequin]$ sudo nano /etc/profile
...
PATH="$PATH:/usr/local/bin/sequin"
...

It doesn't work! See this error message when trying to run sequin

[user@host sequin]$ ./sequin
sequin: error while loading shared libraries: libXm.so.3: cannot open shared object file: No such file or directory

And this library is not in the default repositories:

[user@host sequin]$ yum provides 'libXm.so.3'
Loaded plugins: langpacks, presto, refresh-packagekit
No Matches found

We have to install the 32-bit version from the package openmotif, and since it is one version newer, make a symbolic link. But this package is not in the usual repositories, we need to add the rpmfusion repository.

[user@host sequin]$ sudo yum localinstall --nogpgcheck http://download1.rpmfusion.org/free/fedora/rpmfusion-free-release-stable... http://download1.rpmfusion.org/nonfree/fedora/rpmfusion-nonfree-release-...
...
Installed:
  rpmfusion-free-release.noarch 0:13-4
  rpmfusion-nonfree-release.noarch 0:13-4
[user@host sequin]$ sudo yum install openmotif.i686
...
Installed:
  openmotif.i686 0:2.3.3-1.fc14

Dependency Installed:
  libXp.i686 0:1.0.0-16.fc15

[user@host sequin]$ sudo ln -s /usr/lib/openmotif/libXm.so.4 /usr/lib/libXm.so.3

September 21, 2011

In case it helps anyone else, to install the Roche 454 sequence analysis software (gsAssembler or newbler, gsMapper, etc.) on a computer running 64 bit Fedora 15, there were a few libraries that needed to be installed first, but a necessary condition to get this to work for me was to first enable both the "updates" and "updates-testing" repositories. This is done using
Applications → System Tools → Add/Remove Software → System → Software Sources → Software Sources

Then, this command installed the necessary libraries, along with a number of dependencies:

sudo yum install zlib.i686 libXi.i686 libXtst.i686 libXaw.i686

The install then went smoothly.

However, the "454 Sequencing Applications" menu did not appear in the main Applications menu. To make them show up (and I am operating in "Fallback mode" if that makes a difference), I also needed this command

sudo ln -s /etc/xdg/menus/applications-merged /etc/xdg/menus/applications-gnome-merged

For reference, here is the error I received before enabling all repositories:

	Error: Protected multilib versions: libgcc-4.6.0-10.fc15.i686 != libgcc-4.6.1-9.fc15.x86_64

I am posting this in case it happens a THIRD time and google will then lead me here (hopefully).

A new gbrowse database I was setting up shows only a big red "Not Found" error. Not helpful.

Apache log shows lines like:

[Mon Mar 14 10:00:09 2011] [error] [client 128.128.128.128] indexing was interrupted, so unlinking /var/www/html/gbrowse2/databases/dbnamehere/directory.index at /usr/local/share/perl5/Bio/DB/Fasta.pm line 1053., referer: http://cranberry.vcru.wisc.edu:7280/cgi-gb/gbrowse/mynewdbnamehere/

Still not so helpful.
I made a short perl program with just this essential part:

use Bio::DB::Fasta;
  my $db      = Bio::DB::Fasta->new('/var/www/html/gbrowse2/databases/mynewdbnamehere');

This gave useful error messages!

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Each line of the fasta entry must be the same length except the last.
    Line above #1682 '
..' is 19 != 52 chars.
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:368
STACK: Bio::DB::Fasta::calculate_offsets /usr/local/share/perl5/Bio/DB/Fasta.pm:770
STACK: Bio::DB::Fasta::index_dir /usr/local/share/perl5/Bio/DB/Fasta.pm:593
STACK: Bio::DB::Fasta::new /usr/local/share/perl5/Bio/DB/Fasta.pm:488
STACK: ./test.pl:11
-----------------------------------------------------------
indexing was interrupted, so unlinking /var/www/html/gbrowse2/databases/cucumbermito/directory.index at /usr/local/share/perl5/Bio/DB/Fasta.pm line 1053.

So, the actual problem was that the FASTA file had lines of different lengths! Fixed that and the problem is gone.

December 11, 2010

Some random notes about Blast2GO:

To get around this error message in Blast2GO:
Error in blast result (XML has over 6000 lines

Run the BLAST step again, but reduce the number in the "Number of Blast Hits" box.

October 11, 2010

We have some WRT54GL routers running OpenWRT Linux, and modified to record temperatures with 1-Wire sensors in the greenhouse. There is no wired network there, so we need to use the UW Wireless network that is available. There is a hard to find page with information about setting up WiscVPN on linux here: http://kb.wisc.edu/helpdesk/page.php?id=9120

But when connecting to DoIT VPN, the connection drops after about 30 minutes, and cannot be reconnected for another 45-60 minutes.

The connection drops when DHCP renewal occurs, and appears to only work again when the DPD (Dead peer detection) times out and declares the peer dead. I say this because if you disable dead peer detection, you are locked out for the entire day.

This web page had an answer: http://svn.dd-wrt.com:8000/dd-wrt/ticket/973
Add this firewall rule to /etc/firewall.user

# Rule to prevent VPN dropping when DHCP is renewed
iptables -I INPUT -p udp --dport 68 -j ACCEPT

October 2, 2010

In case it helps anyone else, to install the Roche 454 sequence analysis software on a computer running 64 bit Fedora 13, there were a few libraries that needed to be installed first:

glibc.i686 zlib.i686 libXi.i686 libXtst.i686 libXaw.i686

Roche software version was 2.3

So these two commands took care of that (I could have combined them into one of course):

$ sudo yum install glibc.i686
...
Installed:
  glibc.i686 0:2.12-3

Dependency Installed:
  nss-softokn-freebl.i686 0:3.12.6-3.fc13

Dependency Updated:
  glibc.x86_64 0:2.12-3
  glibc-common.x86_64 0:2.12-3
  glibc-devel.x86_64 0:2.12-3
  glibc-headers.x86_64 0:2.12-3

$ sudo yum install zlib.i686 libXi.i686 libXtst.i686 libXaw.i686
...
Installed:
  libXaw.i686 0:1.0.6-4.fc12
  libXi.i686 0:1.3-2.fc13
  libXtst.i686 0:1.0.99.2-3.fc12
  zlib.i686 0:1.2.3-23.fc12

Dependency Installed:
  libICE.i686 0:1.0.6-2.fc13
  libSM.i686 0:1.1.0-7.fc12
  libX11.i686 0:1.3.1-3.fc13
  libXau.i686 0:1.0.5-1.fc12
  libXext.i686 0:1.1.2-2.fc13
  libXmu.i686 0:1.0.5-2.fc13
  libXpm.i686 0:3.5.8-2.fc13
  libXt.i686 0:1.0.7-1.fc13
  libuuid.i686 0:2.17.2-7.fc13
  libxcb.i686 0:1.5-1.fc13

Dependency Updated:
  libblkid.x86_64 0:2.17.2-7.fc13
  libuuid.x86_64 0:2.17.2-7.fc13
  util-linux-ng.x86_64 0:2.17.2-7.fc13

September 6, 2010

Contents

[A]. Make space on the hard drive

[B]. Create a bootable USB flash drive with Ubuntu 10.04.1 LTS (Lucid Lynx)

[C]. Boot with and install Ubuntu

[D]. Issues

[D.1]. Wired ethernet port does not work. [Solved (90%)]

[D.2]. Battery is not detected

[D.3]. Sleep/restore does not work

[D.4]. Touchpad suddenly stopped working. [Solved (I was stupid)]

[D.5]. Setting screen brightness from keyboard locks up everything [partial solution]

[E]. Notes

[A]. Make space on the hard drive

Boot up with included Windows 7 Starter.

When you can finally get to the point where you can do something,

open the Start menu

right click on "Computer"

select "Manage"

select "Disk Management"

right click on the "Acer (C:)" partition

select "Shrink Volume..."

wait for "Querying volume for available shrink space, please wait..."

shrink the partition as much as possible. This leaves about half of the drive available.

shut down Windows

[B]. Create a bootable USB flash drive with Ubuntu 10.04.1 LTS (Lucid Lynx)

Download the Netbook Live CD image from:

http://releases.ubuntu.com/10.04.1/

"PC (Intel x86) netbook live CD"

And also download the Universal-USB-Installer

Instructions are here:

http://www.ubuntu.com/desktop/get-ubuntu/download

( i.e. Download the Universal USB Installer from:

http://www.pendrivelinux.com/downloads/Universal-USB-Installer/Universal-USB-Installer.exe

I used version 1.7.9

It is probably safest to select "Check this box if you want to format the Drive"

And it takes less time if you select the "No Persistence" option )

[C]. Boot with and install Ubuntu

Insert USB flash drive in netbook

Turn netbook on

Press F2 key to enter BIOS setup

Use right arrow to select "Boot" option

Use up or down arrow to selet "USB HDD: your specific model may appear here"

Use F6 key to move it to the top of the list

Press F10 to save and exit

Select "Yes"

After reboot, you will have just a few seconds to select the "Install to a Hard Disk" option

with the up/down arrows

Hopefully all goes well and you will eventually get an "Install" screen

1. select language

2. select time zone

3. select keyboard layout

4. "Specify partitions manually (advanced)"

I want to keep the "/home" partition separate, and leave room for another operating system,

so I need to set this up manually

I had:

   /dev/sda1   ntfs   13958 MB    ( this is the Windows Recovery partition )
   /dev/sda2   ntfs   104 MB      ( this is the Windows boot partition I assume )
   /dev/sda3   ntfs   118049 MB   ( this is the Windows 7 partition )
   free space         117945 MB

  Select the "free space" row and click the "Add..." button
  Type for the new partition:                      Logical (already 3 primary partitions and 4 is maximum possible)
  New partition size in megabytes (1000000 bytes): 256
  Location for the new partition:                  End
  Use as:                                          Ext4 journaling file system
  Mount point:                                     /boot

  Select the "free space" row and click the "Add..." button
  New partition size in megabytes (1000000 bytes): 8000
  Location for the new partition:                  Beginning
  Use as:                                          swap area
  Mount point:                                     

  Select the "free space" row and click the "Add..." button
  New partition size in megabytes (1000000 bytes): 24000
  Location for the new partition:                  Beginning
  Use as:                                          Ext4 journaling file system
  Mount point:                                     /

  Select the "free space" row and click the "Add..." button
  New partition size in megabytes (1000000 bytes): 24000
  Location for the new partition:                  Beginning
  Use as:                                          Ext4 journaling file system
  Mount point:                                     /

  Select the "free space" row and click the "Add..." button
  New partition size in megabytes (1000000 bytes): 24000  
  Location for the new partition:                  Beginning
  Use as:                                          Ext4 journaling file system
  Mount point:                                     /fedora ( for another operating system later )

  Select the "free space" row and click the "Add..." button
  New partition size in megabytes (1000000 bytes): 61688  ( all remaining space )
  Location for the new partition:                  Beginning
  Use as:                                          Ext4 journaling file system
  Mount point:                                     /home

5 (there was no screen 5)

6. enter username information

7. (there was no screen 7)

8. Press the "Install" button

when finished, remove USB drive (otherwise you will boot from the USB again)

and Restart

[D]. Issues

[D.1]. Wired ethernet port does not work.

I call this 90% solved, because you will have to do this again every time there is a kernel update!

[Solved (90%)] Reference: http://ubuntuforums.org/archive/index.php/t-1505697.html

[D.2]. Battery is not detected

In /var/log/messages:

[    0.351466] ACPI: Battery Slot [BAT1] (battery absent)

Some relevant bug reports:

April 7, 2010: https://bugzilla.kernel.org/show_bug.cgi?id=15707#c2

Aug 22, 2010: http://www.uluga.ubuntuforums.org/showthread.php?p=9917237

Sep 9, 2010: same issue on Mandriva http://forum.mandriva.com/viewtopic.php?t=131642

Oct 2, 2010: http://www.mail-archive.com/ubuntu-bugs@lists.ubuntu.com/msg2544612.html

Oct 2, 2010: http://www.mail-archive.com/acpi-bugzilla@lists.sourceforge.net/msg31499...

Ubuntu WIKI lists bios versions, ethernet problem, battery not detected problem

[D.3]. Sleep/restore does not work

Some relevant bug reports:

• http://www.mail-archive.com/ubuntu-bugs@lists.ubuntu.com/msg2544673.html
• https://bugs.launchpad.net/ubuntu/+source/linux/+bug/653524
  
  This link has a fix that works mostly (about 3 out of 4 times the computer will not suspend)

[D.4]. Touchpad suddenly stopped working.

[Solved]
Press "Fn F7" key combination to turn it back on. (D'oh!)

[D.5]. Setting screen brightness from keyboard locks up everything

The first strange thing, under Windows 7, the Fn+solid-sun combination (on left-arrow) makes the screen Darker
while the Fn+sun-with-black-center (on right-arrow) makes the screen Brighter, the opposite of what
anyone would expect based on those little icons.

But Fn+either of these locks up the system totally under Ubuntu. A power down is required to restart.

The Fn+volume keys do not lock up the system, and function correctly.

[Partial Solution] from http://ubuntuforums.org/showthread.php?t=1213302

Pass in "acpi_backlight=vendor" to the kernel on boot as described there (other parameters don't seem to have any effect).

Brightness does not change, but at least the computer doesn't lock up.

This message appears in /var/log/kern.log:

ACPI: Failed to switch the brightness

Bug report at https://bugs.launchpad.net/dell/+bug/568611

If I also pass in acpi_osi='Linux' as described in message #8 of the same link,
I can also see the brightnes slider.

Still no change in brightness, however!

("acpi_osi='Linux'" without "acpi_backlight=vendor" causes a different horrible seizure at the login screen)

(List of kernel parameters)

[E]. Notes

• I have bios version V1.01, I found this report that version 1.0.3 or 1.0.6 are bad news, but 1.0.8 is ok
• External and internal images of the AO521 can be found here

August 16, 2010

How to edit /etc/fstab when at Fedora "Repair filesystem" prompt?

Source: http://www.techiegyan.com/?p=86

Use following command to mount the filesystem with writable permission:

Repair filesystem # mount -w -o remount /

February 15, 2010
Updated Oct 30, 2010 to retry incomplete download, check for incomplete files, and handle all root level folders

I wanted to automate the download of sequences from the University of Wisconsin - Madison Biotech Center server.
It was a bit tricky, with all the authentication through DoIT and javascript and redirection - but I finally came up with a Perl program that does it.
On the off chance anyone out there is googling for such a program, here it is.

 

other keywords: Linux, curl, backup, sequencing facility, unattended, FileVistaControl

February 4, 2010

Keywords: power failure
Did your Eppendorf Mastercycler Gradient 5331 suddenly go dead? And it isn't the fuse? And it IS plugged in?

Two of ours have failed in this manner, but the repair costs only about $10.
For the benefit of anyone who may have this same problem, it was the inrush current limiter.

This image shows the location of the current limiter, here labeled SL15 20004 (Amtherm, Inc.)

A closeup

This part was not available, I replaced it with a MS22 20005, Digi-Key part number 570-1007-ND

September 28, 2009

If you need a hand in the garden, try a carrot... (groan)
This was published in the Daily Mail on Sept 21, 2009:

You've got to hand it to Mother Nature as gardener digs up five-fingered carrot

September 2, 2009

This summer the insulation on the pipes carrying the coolant to the coolers, cold rooms, and seed storage room in the building was replaced. The coolers were shut down on June 4, and were working normally again on Aug. 24, 2009.
Taking advantage of the now obsolete Cat 3 network wiring left behind after last summer's network upgrade, a new low-cost system is available to monitor their temperatures.
You can view current and past temperatures at this address
http://www.vcru.wisc.edu/1wire
as well as some information about the system.

August 27, 2009

Some obscure technical information for anyone interested in writing software to monitor their Revco ultracold freezer. This information does not seem to exist anywhere else on the internet, so I am posting it here just to get it out there.

The interface is a standard RS232 serial port on the bottom back side of the freezer. (See Attached image) If you don't have this interface (not all freezers do) then the remainder of this information is probably not of much value to you.

Disclaimer: The following information was obtained by trial and error. Errors are of course likely.

Data packet format information:
To receive a data packet, a 'T' is transmitted
The received packet is always 16 characters, which encode 8 bytes in
hexadecimal. No carriage returns or anything else are sent or received.
Data rate is fixed, at 9600, N-8-1.

Packet format:
sample packet '0300599566315284'
first 2 bytes encode status flags, described below
next 2 bytes encode current temperature, encoding described below
next 2 bytes unknown, my guess is first stage of refrigeration
next 2 bytes encode set point temperature

Encoding:
Temperatures are encoded as a 2-byte integer, and can be converted
to degrees Celsius with the formula
DegC := (value / 129) - 243.7519
This was determined by entering set points, and looking at the
encoded set point value. The divide by 129 looks strange (why not
128?), but it works from -50 to -80 at least. Values this was
based on: 5284 for -80 setpoint, 5305 for -79, 5386 for -78,
5407 for -77, 5488 for -76, 61A2 for -50.

Flags:
The first 2 bytes encode flags as follows
bit 15 Temp Alarm Status RTD TEST
bit 14 Temp Alarm Status LOW
bit 13 Temp Alarm Status HIGH
bit 12 Unknown
bit 11 Unknown
bit 10 Unknown
bit 9 Seems to be compressor running, second stage
bit 8 Seems to be compressor running, first stage
bit 7 Unknown
bit 6 Unknown
bit 5 Unknown
bit 4 Filter Status CLEAN
bit 3 Fuse Status CHECK
bit 2 Unknown
bit 1 Power Status FAIL
bit 0 Battery Status LOW

NVRam information:
To receive non volatile ram contents, an 'N' is transmitted.
Sample returned data:

<CR><LF>
............... nvram contents......................<CR><LF>
addr x0 x1 x2 x3 x4 x5 x6 x7 x8 x9 xa xb xc xd xe xf<CR><LF>
0000 52 84 5C A5 4D 71 01 83 FF FF FF FF 01 04 5E 00 <CR><LF>
0010 FF FF 03 03 FF FF FF FF FF FF FF FF FF FF FF FF <LF><CR><LF><CR>

A total of 222 bytes ($DE) is transmitted
Address 0..1 encodes set point temperature as above @ bytes 116, 117, 119, 120
2..3 encodes High Limit temperature @ bytes 122, 123, 125, 126
4..5 encodes Low Limit temperature @ bytes 128, 129, 131, 132
temperature encoding is the same as for data packet temperatures.

March 18, 2009

Señor Inyeccion is currently on strike, demanding better HPLC music.