Questions about this FTP site should be directed to system@ftp.bio.caltech.edu.
Anonymous uploads ("put") to this site are blocked.
Directory contents as of 19-OCT-2000:
ABITOOLS.ZIP
Tools and documentation for handling ABI files in a VMS
environment.
ABIBREAKOUT.FOR Fortran 77 program which converts an ABI trace file to
a text format. Read the comments at the top before using it.
ABIPRINTOUT.FOR,ABIPRINTOUT.CMD,ABIPRINTOUT.TXT,ABI_UTILS.FOR
Fortran 77 program which prints traces through
the GCG graphics interface after extracting
them from an ABI file. Can also use PHRED output
for better base calling.
EXAMPLE_ABIPRINTOUT.PS
One page of output from ABIPRINTOUT
PROCESS_ABI_FILES.COM
DCL procedure used at Caltech to batch
process ABI files, run them through PHRED,
and produce and print trace files for the
end users.
ABI.TXT Notes derived from binary spelunking in the
ABI files to figure out their organization.
DATASNIFFER.FOR Fortran 77 program used to figure out the
structure of ABI files. (Unlikely it
will work without modification on anything
other than a VMS machine.)
Use BINARY FTP to transfer
AUCTION.ZIP Small scale auction system, for use with the OSU Decthreads
webserver. (It could probably be modified to work with other
OpenVMS servers, but not on anything else, since the scripts
are in DCL.)
Use BINARY FTP to transfer.
FASTTRANS.C Program that translates ORF's or whole frames for FASTA
format DNA (or RNA) files to Protein.
Use ASCII FTP to transfer.
GIBBS.ZIP VMS port of the NCBI's Gibb's software. Contains .exe for
VMS/AXP 6.1 + DECC 4.1, also source code, demo, build
instructions, and porting notes.
Use BINARY FTP to transfer.
GLE_3_3H_VMS_ALPHA.ZIP
VMS port of GLE version 3.3H. Works correctly on ALPHA (other GLE ports
I tried do not.) GLE is a very nice graphing tool, semi-
interactive (modify "program", hit button to plot, repeat until
done.) X11, Postscript, and other formats supported. More
controllable than GNUPLOT, makes nicer plots (personal opinion,
obviously.)
Use BINARY FTP to transfer.
GCGCGM.ZIP CGM graphics driver for the GCG molecular biology package.
.TAR Example output from driver in PLOTTEST.CGM
Use BINARY FTP to transfer.
GCGGIF.ZIP GIF graphics driver for the GCG molecular biology package.
.GIF Example output from driver in PLOTTEST.GIF
Use BINARY FTP to transfer.
GNU_M4-1_4_VMS.ZIP
VMS port of gnu m4 preprocessor. Result of a merge of the
preexisting 1.2 port and the current 1.4 distribution.
GNUPG1_0_2_VMS.ZIP
VMS port of GNU PG application.
ICALCV.ZIP Slightly modified version of the ICALC program. On VMS systems
it will put the results of up to 10 calculations, specified on
the command line, into a symbol ICALC_OUT (comma separated, if
more than one result). For the interactive mode, it will only
put the LAST result into that symbol.
MACBIN_XBIN_VMS.ZIP
OpenVMS versions of the XBIN and MACBIN programs. XBIN
extracts the resource, data, and information forks from a .hqx
file. MACBIN assembles the three files into a single MacBinary
file.
Use BINARY FTP to transfer.
MAIL_MAI_TOOLS.ZIP
Tools for generating a mail.mai file from a set of
mail$xxxxxxx.mai files. Useful for "repairing" a users
mail files when mail.mai has been deleted/destroyed on
a system with incomplete or no backups.
Use BINARY FTP to transfer.
MAKE_OPT_FROM_OLB.COM
This DCL procedure analyzes an object library file (.OLB)
and produces from it a linker option file (.OPT) which may
be used to link together a shareable image. Shareable images
may be linked into other programs, and as the name states,
shared between them. This can save a considerable amount of
memory since the code present in the image need only be present
once in memory, not once for each application which uses it.
Use ASCII FTP to transfer.
MINIPROC_2_00_SOURCE.ZIP
A general purpose file preprocessor. Very strictly ANSI C,
known to compile and run on OpenVMS and Irix. Works 99%
with CodeWarrior Pro 2 on Windows and WNT (except for
stat() based functions, which the compiler doesn't have.)
Binaries for this program for many platforms are available,
see below.
Use BINARY FTP to transfer.
MINIPROC_2_00_D_UNIX_DECC.GZ
MINIPROC_2_00_IRIX_5_3.GZ
MINIPROC_2_00_OVMS_ALPHA_6_2.ZIP
MINIPROC_2_00_SOLARIS_GCC.GZ
MINIPROC_2_00_WIN32_CODEWARRIOR.ZIP
Binaries for miniproc for several platforms. You will also
need to pick up the MINIPROC_2_00_SOURCE.ZIP file.
Use BINARY FTP to transfer.
MMAIL.COM
Demo procedure demonstrating how to send MIME mail messages
(as generated by mpack) via MULTINET.
Use ASCII FTP to transfer.
MNEWS.COM
Demo procedure demonstrating how to send a news post to
a NEWS server with a MIME mail messages
(as generated by mpack) via MULTINET.
Use ASCII FTP to transfer.
MPEGPLAY_2_3_VMS.ZIP
VMS port of Mpeg_play 2.3 using Compaq C V6.2-007 on OpenVMS
Alpha V7.2-1.
Use BINARY FTP to transfer.
MYBENCHMARK.ZIP
Small set of programs to benchmark simple read/write
performance on OpenVMS and elsewhere.
NETPIPE_2_3.ZIP
VMS port of TCP variant of Netpipe. Contains source
code and binaries. Tests packets only up to 65Kb on VMS.
Use BINARY FTP to transfer.
UNZIP with /VMS
NETPIPE_2_4beta.ZIP
VMS port of TCP variant of Netpipe. Contains source
code and binaries. Tests packets only up to 65Kb on VMS.
This version works better on Linux on a DS10.
Use BINARY FTP to transfer.
UNZIP with /VMS
NODEINSTALL.TGZ
.tar.gz file containing a /node-install directory for Linux/Alpha.
Contains scripts and files for configuring compute nodes on a
Beowulf cluster under Redhat 6.2. See INSTRUCTIONS once it's
unpacked into /node-install.
Use BINARY FTP to transfer.
OPENVMS.DIR
Directory containing a bunch of OpenVMS utilities in DCL.
PATCH_WITH_DIFF.COM
Procedure to use the SUM/SLP editor with diff files.
Use ASCII FTP to transfer.
PGSQL_VMS_PARTIAL_PORT.ZIP
Partial port of PosgreSQL to VMS. Large swaths compile cleanly
but other chunks are Unix specific and need to be replaced.
Use BINARY FTP to transfer.
PIPE_COLUMNADD.ZIP
Small fortran program which reads from sys$input, writes to
sys$output and sums numbers down columns in the records,
outputting each time it hits a blank line. Understands how
to carry on a decimal, and recognizes OpenVMS time formats (
some). Does not know about exponents!
Use BINARY FTP to transfer.
PASSWD_TO_NAMES.NAWK
NAWK program for converting a Unix passwd file to the "names"
database format used by the campuswide Name Space system.
PESTFIND.ZIP
ANSI C port of M. Rechsteiner's PESTFIND program. Test files.
DCL procedures to wrap it for use with GCG package.
PHYLO_WIN_VMS.ZIP
VMS port of the PHYLO_WIN phylogeny program. Includes source
and binaries for OpenVMS/Alpha 6.2.
Use BINARY FTP to transfer.
PRINT_TO_WINDOWS.ZIP
DCL procedures that wrap smbclient and allow VMS machines to
print to Windows printers.
Use BINARY FTP to transfer.
PSCAL.ZIP VMS port of PCAL program - prints nice monthly calendars
in POSTSCRIPT.
Use BINARY FTP to transfer.
PKZ204G.EXE
MSDOS zip program, from Oak.Oakland.edu Simtel mirror site.
Use BINARY FTP to transfer.
REP_CLIENT2.ZIP
Source for web POST stuffing program, modified from the
original from the NCBI. This variant reads a sort of
script file, with data corresponding to form fields,
and massages it into the right format, then retrieves
the web server's response.
Use BINARY FTP to transfer.
RFINDPATTERNS.FOR,.TXT,.CMD
Findpatterns variant - it extracts the pieces it finds into
separate files.
Only sites with valid GCG licenses should retrieve this program!
Use ASCII FTP to transer.
RTFTOHTML.ZIP
VMS port of Chris Hector's RTFtoHTML software. Contains .exe for
VMS/AXP 6.1 + DECC 4.1, also source code, docs, and build
instructions.
Use BINARY FTP to transfer.
SAFDEC.KBD Much improved keyboard file for Micro-X Win. This one puts
the key functions in the right positions, as much as possible
like an LK series keyboard. Still need to use a MICROX_WIN modmap
with this keyboard, but numlock works correctly.
Use BINARY FTP to transfer.
SEAT.ZIP
Autologout and billing software (CRUDE) for use on
Unix workstations. Your mileage may vary :-).
Use BINARY FTP to transfer.
SERVERCONFIG.ZIP
System for configuring remote X11 servers to use OpenVMS
clients. Modmaps for MacX and MicroX-Win included, as
are sample *.VUE$DAT files, and an experimental "console
time limiter".
Use BINARY FTP to transfer.
SHOTGUN.ZIP
Software for emulating shotgun sequencing projects. May be
used for cost estimation. Includes data emulating such a
project for the human genome.
Use BINARY FTP to transfer.
SHOWMESH.C
Simple program for processing GCG assembly projects and
classifying each clone into IntraContig, IntraMesh,
or left_/right_missing.
Use ASCII FTP to transfer.
SMBCLIENT.ZIP
OpenVMS 7.1/Alpha Samba 1.9.19 SMBCLIENT. Runs on top of UCX
or UCX emulation. Connects to NT 4.0 sp 3 and current Unix
Samba servers. PRE-ALPHA. Please report bugs.!
Syntax: smbclient "-L" machine "-U" username
smbclient "\\machine\resource" "-U" username
Use BINARY FTP to transfer.
SSLEAY_8_1_FOR_OSU.ZIP
Files and instructions for building SSLeay .081 for use with
the OSU DECthreads webserver.
Use BINARY FTP to transfer.
SYSUAF_TO_NAMES.COM
DCL script for converting a SYSUAF.LIS file to the "names"
database format used by the campuswide Name Space system.
TCONTROL.ZIP
TCONTROL sets/reads bits on a serial line. Includes
UPS_MONITOR.COM, for monitoring a UPS through TCONTROL
and shutting down the system gracefully on power failure.
Use BINARY FTP to transfer.
TESTURLS_FETCH_HTTP.ZIP
TESTURLS is a DCL procedure that scans through HTML looking
for bad links. It can be useful for keeping VMS Web sites
in order. It uses a variant of FETCH_HTTP that has been
modified to allow timeouts and retrieval of header status
into DCL symbols.
TWIN_3_0_10_VMS_001.ZIP
Partial port of the "Twin" windows emulation software.
Use BINARY FTP to transfer.
UNZ512X.EXE
MSDOS unzip program, from Oak.Oakland.edu Simtel mirror site.
Use BINARY FTP to transfer.
VMSHELPINDEX.ZIP
Tools for feeding VMS HELP files through Bruce Tanner's indexer
so that the resulting indexed files may be served through the
HELPgateway.
Use BINARY FTP to transfer. Unpack with UNZIP/VMS.
VMS_MPACK_1_5.TAR
VMS port of MPACK. Use to pack and unpack MIME files.
Use BINARY FTP to transfer.
VMS_TO_UNIX.C
DCL utility that translates VMS file specs to Unix File specs
and, if there is just one, leaves the name in the symbol
UNIX_FILENAME.
Use ASCII FTP to transfer
X11PERF_15.ZIP
Port of X11perf 1.5 for VMS.
Use BINARY FTP to transfer.
XLDLAS.ZIP VMS port of XLDLAS 0.85 program. Also needs GNUPLOT to work
properly. Can use TEX if you have it (not tested).
This is a data analysis program, does some statistics. Runs on
top of XFORMS.
Use BINARY FTP to transfer.
XWIN_MAN.PS
Micro X-Win manual in postscript format.
Use ASCII FTP to transfer.
XBIN.ZIP
Port to OpenVMS of a Unix (de)binhex program. Useful for
extracting RTF files and others that don't have anything
important in the resource fork.
Use BINARY FTP to transfer.
XTERM021_MODERN.ZIP
USE XTERM_VMS_122.ZIP instead, it works much better!
Modified variant of XTERM021 port. This one will build
on OpenVMS/Alpha with modern versions of DEC C (6.x and
higher.) Objects and an executable are included which were
built on OpenVMS 7.2-1.
Use BINARY FTP to transfer.
ZIP file constructed with /VMS.
XTERM_VMS_122.ZIP
Modified variant of current Linux variant of Xterm plus
XMU and XAW3D libraries that work with it. It
will build on OpenVMS/Alpha with modern versions of DEC C (6.x
and higher.) Objects and an executable are included which were
built on OpenVMS 7.2-1.
Use BINARY FTP to transfer.
ZIP file constructed with /VMS.
XTERM_VMS_122_TOP.ZIP
Like the preceding ones, but including only the Xterm
specific source code files.
Use BINARY FTP to transfer.
ZIP file constructed withOUT /VMS.