read_cyclops_win.html = this file
cyclops is a graphical program developed at the Sanger Centre for comparing a whole chromosome assembly with the corresponding physical and/or genetic maps. The user can move a graphical representation of selected contigs around a window (called a "SandBox") to try to align them with the physical and/or genetic maps of the chromosome. The program also shows pUC bridges from the ends of contigs and allows the user to "tie" pairs or groups of contigs together and move them around the SandBox as a single unit. Cyclops is mainly used for the finishing process and there is no annotation associated (Artemis is used for Annotation).
For additional cyclops documentation:
http://www.sanger.ac.uk/Software/sequencing/docs/harper/cyclops.shtml
Download: cyclops_win.zip contains a Microsoft
Windows 95/98/NT/2000 "freestanding" executable of the Sanger
Centre cyclops program written in Perl/Tk and an old dataset of mal4. Please
download the updated dataset:
ftp://ftp.sanger.ac.uk/pub/pathogens/malaria2/cyclops-data/
Instead of running cyclops.exe which depends on specific Microsoft DLL, you
can alternatively download the cyclops software from the Sanger Centre's FTP
site:
ftp://ftp.sanger.ac.uk/pub/pathogens/software/sequencing/cyclops/
and then install perl from:
cyclops.exe have been tested on: Windows 2000, Windows NT, and Windows 95 only so far.
Run: at the command prompt type: cyclops.exe mal4
For example:
C:\TEMP>cyclops mal5
# Assembly mal5: reading basic data
# Assembly mal5: reading split data
# Assembly mal5: reading YAC data
# Assembly mal5: reading STS data
# Assembly mal5: reading pUC data
# Assembly mal5: reading physical map data
# Assembly mal5: reading STS map data
--> The graphical user interface should appear, if NOT, please setup the
Display Environment Variable.
Cyclops expects a display environment variable pass in. So, remember to set your Environment Variables:
-------------Windows NT------------------------------------------------
-On NT: Start --> Settings --> Control Panel --> System --> Environement
tab --> Add "Display" variable with the value "0:0" (no
quotes) for the
xwindow display setting.
-------------Windows 2000------------------------------------------------
-On Windows 2000: Start --> Settings --> Control Panel --> System
-->
Advanced tab --> Environment Variable button --> Either set the user
variable or system variables: --> Add "Display" variable with the
value
"0:0" (no quotes) for the xwindow display setting.
-------------Windows 95/98------------------------------------------------
-On Windows 95/98: (a lot more complicated to configure)
1a. Edit Config.sys and add the following line:
SET Display=0:0
SET TEMP=C:\temp
SET TMP=C:\temp
or
1b. Obtain a copy of WINSET.EXE
See Microsoft Proudct Support Services Article
ID: Q140574
at the command prompt type:
winset Display=0:0
2. Run the test program
cyclops mal4
3. Does step # 2 work, if so congratulations. Else continue with Step #4
4. If you get "StartUp Error: Failed to Extract and Load Perl Runtime
Dependencies", then:
4a. Is PerlCRT.dll (The Perl C Runtime Library) installed on your machine?
--> No, then download a local copy here:
PerlCRT.dll and add it to c:\Windows\System\
Try running cyclops mal4 again, if it still doesn't work, continue to the
next step
--> Yes, go to step # 4b
4b. Are MS Visual C Runtime library files installed in C:\Windows\System?
The files are MSvcrt.dll, Msvcrt20.dll, and Msvcrt40.dll
--> No, then download a local copy here: msvcrt.exe
And run the self extracting program, to get the 3 dll and copy to
C:\Windows\System
Try running cyclops mal4 again, if it still doesn't work, continue to the next
step.
--> Yes, go to step #4c
4c. Is C:\temp set to be with read/write privilege?
--> No, then set read/write privilege for the temp directory on your
machine. This can be determined by right clicking on a directory folder
with your mouse and selecting "Properties" and make sure the Read
Only
attribute is not selected.
Or at the dos prompt:
attrib c:\temp
It should be blank.
Try running cyclops mal4 again, if it still doesn't work, continue to the next
step.
--> Yes, go to step #4d
4d. Finally, if step #4a-c doesn't work at all. Winzip/Pkunzip and copy the
content of bin_plug_Perl_Bin at:
bin_plug_Perl_Bin.zip
to C:\Windows\System directory. However, this should work since it adds all
of the possible run time libraries,etc. to your path, but it adds a lot
of extra
junk!!!
The data is available at the Sanger Centre ftp site in two compression format: .tar.gz (for Linux/Unix users) and .zip (for Windows 95/98/NT/2000 users).
Winzip for Windows is capable of uncompressing both compression format
http://www.winzip.com/
-Add code for wincron + perl ftp for MS Windows system for automated updates of Cyclops file.
If you have additional questions, not answered in this document, send an email to: huynh@ncbi.nlm.nih.gov