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.