Schneider Lab
origin: 2011 Sep 03
updated: 2012Apr05_21:11:29
| Program | Synopsis | Details |
| README-toolkit.txt | WEB PAGE: toolkit.html | |
| a | Place the file into your 'a' directory: echo "Place the file into your a directory:" |
usage: a [-cl] [-look] [-r] [-s] [-q] [file] |
| alt | Update the alt tags in html files. |
usage: alt [-l][-v][-n][-N][-r][-h][-a][-b][-i][-c] [list] |
| atc | atchange the argument, clear screen each time |
usage: atc [at change file] [function to do] |
| atchange | WEB PAGE: atchange.html | |
| atchange.macosx | see the description in the source code | |
| au | see the description in the source code | |
| aw | Watch the a directory across the net and transfer files |
usage: aw [options] |
| bar.long | see the description in the source code | |
| bar.sed | see the description in the source code | |
| bar.short | see the description in the source code | |
| bargreater.sed | see the description in the source code | |
| bibtex2pmcid | see the description in the source code | |
| browse | This script opens the default browser to the given url. |
usage: browse [url] [browser] |
| browserurl | Set your browser to the given url. |
usage: browserurl [url] |
| bs | Produce backspaces to control a terminal display. |
usage: bs (-n [number]|-s [string]|) |
| buffer | Put the file into the Mac cut/paste buffer. |
usage: buffer [file] [top lines to cut] [bottom lines to cut] |
| buffera | see the description in the source code | |
| buffersay | Say a phrase on Mac OS X through a fifo buffer. |
usage: buffersay [phrase] & |
| buffersaykill | buffer say kill: kill any processes still running from buffersay |
usage: buffersaykill |
| cache | cache [-l | -t] [number of files to show] |
usage: cache [item#] [new name] |
| cacheflow | see the description in the source code | |
| cacheget | Capture files from browser (Seamonkey, Firefox?) cache. |
usage: cacheget [type] [number to get] |
| cachetype | see the description in the source code | |
| calaround |
calaround shows the previous, current and next calendar months
WEB PAGE: calaround.html |
usage: calaround [integer1 [integer2]] |
| calc.p | calc(input: in, output: out) | Pascal program: calc Manual Page |
| chmodcp | chmod copy - copy the permissions of one file to another |
usage: chmodcp file1 file2 |
| cl | Clean Latex: remove all files associated with the LaTeX document |
usage: cl [LaTeX document] [NOT ...] |
| clearscreen | Clear the screen and the entire scrollback on a Mac OS X Terminal. |
usage: clearscreen [optional argument] |
| clmn | Fast column grab from a file. clmn takes in a file and a column number and outputs |
usage: clmn [column number] [file] usage: clmn [column number] [file] |
| color | Color a Mac OS X file using the color name or numbers from 0 to 7 |
usage: color [file] [color number or color] |
| column.p | column(input: in, columnp: in, output: out) | Pascal program: column Manual Page |
| cshrc.toolkit | see the description in the source code | |
| dave | echo usage: dave file_name endif | |
| daydate | see the description in the source code | |
| db |
usage: db [file to put in dropbox] |
|
| denplo.p | denplo(data: in, denplop: in, | Pascal program: denplo Manual Page |
| diffdelila | diffdelila finds the differences between the local file |
usage: diffdelila [file of the delila system] [s] [t] |
| diffint.p | diffint(input: in, output: out); | Pascal program: diffint Manual Page |
| diffps |
usage: diffps [file1.ps] [file2.ps] "color1" "color2" |
|
| diffsen | see the description in the source code | |
| difi | Show differences between a file with a version string such as |
usage: difi [file with version string] [-expand][-long][-l][-short][-s] |
| diropen | see the description in the source code | |
| divide | Use the standrd Unix dc program to divide two numbers. |
usage: divide [numerator] [denominator] [decimals] |
| dup | Find files that have the same name except for capitalization. |
usage: dup [arg] |
| dupfolder | see the description in the source code | |
| eh | see the description in the source code | |
| fast | see the description in the source code | |
| fb | see the description in the source code | |
| feak | see the description in the source code | |
| filedate | Express the date of a file as a tomdate. |
usage: filedate [file] [creation] |
| filedatecompare | Compare the dates of the two files. |
usage: filedatecompare [file1] [file2] [-notime] |
| filesize | see the description in the source code | |
| findhere | see the description in the source code | |
| fixpdfname | Fix PDF name. |
usage: fixpdfname |
| fmtdetab | see the description in the source code | |
| fmti | see the description in the source code | |
| focus | see the description in the source code | |
| gef | gef: sets up a tcsh script so that |
usage: gef [name] |
| genhis.p | genhis(data: in, histog: out, genhisp: in, curve: out, output: out) | Pascal program: genhis Manual Page |
| gerr | Get remote remote. |
usage: gerr [file] |
| get | get [file] [as new file name] |
usage: get [file] |
| getp2c | see the description in the source code | |
| goat | GOAT means: go 'a' with timing. echo "GOAT means: go a with timing." |
usage: goat [filehead.type] [Bits per second] |
| gose | Do a google search from the cut/paste buffer. |
usage: gose |
| gpcc | gpc compile: compile a pascal program using gpc |
usage: gpcc [program] [-silent] |
| gpcc-atchange | see the description in the source code | |
| gpcc-atchange-mac | see the description in the source code | |
| grabdelila | Use wget to grab the public Delila programs from |
usage: grabdelila [delila source directory] [binary directory] |
| grablast | see the description in the source code | |
| grabtoolkit | Grab Tom Schneider's Toolkit using wget |
usage: grabtoolkit |
| here | find all 'nowhere' pointers to the current directory |
usage: here [any argument] |
| histo | Store a file into a historic directory with the date tagged onto it. |
usage: histo [file to preserve] [tmp] |
| http | A url (containing "http") in the Mac OSX cut/paste buffer |
usage: http [file] |
| imgalt.p | imgalt(orihtml: in, imgaltp: in, | Pascal program: imgalt Manual Page |
| ip | Print IP address for the current machine |
usage: ip |
| ish | The name ish stands for: IS this SH? |
usage: ish [any argument] |
| l | The l script runs LaTeX on the paper.tex in the current directory. |
usage: l [optional tex file name] |
| lk | link NAME to FILE |
usage: lk [from-name] [to-file] [-hard] |
| lkdelila | link to a delila file, see also get |
usage: lkdelila [file] |
| lkpdf | see the description in the source code | |
| lss | see the description in the source code | |
| lv | see the description in the source code | |
| maf | see the description in the source code | |
| mannoh | Show Unix Manual pages without control-H in vim ("man no H"). |
usage: mannoh [input file] [processed output file] usage: mannoh [man page name] |
| mapquest | Strip out a map from www.mapquest.com |
usage: mapquest |
| medlinebib.p | medlinebib(query: in, medlinebibp: inout, bibformat: out, output: out) | Pascal program: medlinebib Manual Page |
| medquery | Convert a saved PubMed reference page into BibTeX format |
usage: medquery [pubmed page OR pubmed ID OR pubmed central ID] |
| mem | Give the memory status of this Mac OS X computer. |
usage: mem [number] |
| memory.p | memory(input: in, memoryp: in, | Pascal program: memory Manual Page |
| mirror | Make file1 be identical to file2. |
usage: mirror file1 file2 [-v] |
| mkbiglet | see the description in the source code | |
| mkcalc | Execute the calc program and produce a program.results file. |
usage: mkcalc [program.calc] |
| mkcsv | Convert a space delimited ascii table to csv form. |
usage: mkcsv [input file name] [output file name] |
| mklink | see the description in the source code | |
| mklower | see the description in the source code | |
| mkold | see the description in the source code | |
| mkopenhtml | see the description in the source code | |
| mkp2c | see the description in the source code | |
| mktoolkit | Build Tom Schneider's Toolkit |
usage: mktoolkit |
| monthnumber | Convert a 3 letter month to a number |
usage: monthnumber [month as 3 letters] |
| mtc | mtc: convert control M (^M) from Mac OS 9 to cr for Mac OS X |
usage: mtc macos9 macosX |
| mulo | see the description in the source code | |
| myacroread | see the description in the source code | |
| noblank.p | noblank(input: in, out, output: out) | Pascal program: noblank Manual Page |
| noc | see the description in the source code | |
| nohob.p | nohob(input: in, output: out) | Pascal program: nohob Manual Page |
| nom | see the description in the source code | |
| nomultiblank.p | nomultiblank(input: in, out, output: out) | Pascal program: nomultiblank Manual Page |
| nonow | Remove a now link by putting it in /tmp |
usage: nonow [now link name] |
| nor | Convert control Ms to unix carriage returns |
usage: nor [input file] [output file name] |
| nostop | see the description in the source code | |
| noswoosh | see the description in the source code | |
| notes | Create and maintain a Notes.txt file in the current directory. |
usage: notes [any argument] |
| nowhere | WEB PAGE: nowhere.html | |
| np | see the description in the source code | |
| number.p | number(input: in, output: out) | Pascal program: number Manual Page |
| nw | see the description in the source code | |
| o | see the description in the source code | |
| p2crc | see the description in the source code | |
| parent | see the description in the source code | |
| patent | Locate a patent at $source. |
usage: patent [patent number string] |
| pdf [pdf file] |
usage: pdf [pdf file] [new name] |
|
| percent.sed | see the description in the source code | |
| piechart.p | piechart(piechartp: in, pienumbers: in, pieps: out, output: out) | Pascal program: piechart Manual Page |
| pmid2pmcid | Convert the PubMed ID (PMID) number of a paper from PubMed |
usage: pmid2pmcid [PMID] [turn-on-verbose] |
| pms |
pms [arg1] [arg2] [arg3] ...
WEB PAGE: pms.html |
usage: pms "[string]" |
| program | Create a new delila program called 'name.p' echo "Create a new delila program called name.p" |
usage: program [name] |
| ps2jpg | convert ps to jpg using imagemagick |
usage: ps2jpg file.ps [optional edge, in pixels] [optional density] |
| pslocate | Locate errors in a PostScript file |
usage: pslocate [psfile] usage: pslocate [psfile] [range from] usage: pslocate [psfile] [range from] [range to] |
| psv | see the description in the source code | |
| psvi | see the description in the source code | |
| pswrap | Wrap ps files into a single figure. |
usage: pswrap rows cols x0 y0 xshift yshift scale target L ps1 ps2 ... |
| pullpaper | where 'key' is a key for a reference in echo "where key is a key for a reference in" |
usage: pullpaper [-r] [key] |
| pullpmid | Locate a PubMed entry by its ID (PMID). |
usage: pullpmid [PMID|file] |
| pulse | echo -n 'usage: pulse' echo -n ' [-c]' # clear screen | |
| puma | Select one email message from the source file mail box. |
usage: puma [number] [source file mail box] |
| purr | Put remote remote. |
usage: purr [file] |
| pwdsilent | see the description in the source code | |
| rb.p | rb(input: stdin, output: out) | Pascal program: rb Manual Page |
| reading | Set up reading list in DropBox https://www.dropbox.com |
usage: reading [key name] usage: reading -paper [LaTeX name] usage: reading -sync usage: reading [pdf file] usage: reading . usage: reading , usage: reading -a |
| rlog | see the description in the source code | |
| rw | rotate wheel: call with an integer state counter that is increasing |
usage: rw [state counter] |
| save | Save a file/directory into an 'old' directory for backup. echo "Save a file/directory into an old directory for backup." |
usage: save [file] |
| saykey | Say the bibtex key in a pronouncable way. |
usage: saykey [bibtex key] |
| scpa | Transfer the file to a remote directory, put on web. |
usage: scpa [file | -setup | -c | -l | -d | -test | -q ] |
| sd | Side by side diff - sdiff file1 file2 |
usage: sd [file1] [file2] [any third argument will suppress common lines] |
| secure | see the description in the source code | |
| setdelila | see the description in the source code | |
| shell.p | shell(afile: in, shellp: in, bfile: out, output: out) | Pascal program: shell Manual Page |
| shellp | see the description in the source code | |
| showpdf | Show a PDF or postscript file either locally or across the net. |
usage: showpdf [-q] [PDF or postscript file] [-l line-number text_file] |
| skim | Launch Skim PDF reader and set auto controls |
usage: skim [pdf file OR ps file OR -setauto -unsetauto -read] [-bg] |
| skimembed | Embed PDF with marks from Skim into the PDF file itself. |
usage: skimembed [pdf with marks from skim] |
| sl | If the file $sl exists, it contains a list of strings to ignore. Command line equivalent of Spotlight\!\! Command line equivalent of Spotlight\!\! |
usage: sl [string - no quotes needed] [optional directory] # usage: slf [searchstring] usage: sl [string - no quotes needed] |
| slideshow | usage: slideshow [slidelist] [slidelist.html] [image source directory] [...] [slidelist]: an ascii file containing a list of the image files | |
| sore | see the description in the source code | |
| spl | use aspell to spell check a file |
usage: spl [file/word] [uniq] |
| splitsen | see the description in the source code | |
| ss | see the description in the source code | |
| suntera | see the description in the source code | |
| sunweb | see the description in the source code | |
| syncfiles | Grab all files from any computer, put into a specific directory |
usage: syncfiles [user@source_computer] [full_directory_path/] [-dry] |
| tabify.p | tabify(input: in, output: out) | Pascal program: tabify Manual Page |
| talo | see the description in the source code | |
| tarbackup | see the description in the source code | |
| tarball | Wrap file1 into tarball as file2 |
usage: tarball [file1] [file2] usage: tarball file1 |
| tc | see the description in the source code | |
| test.p | test(output: out) | Pascal program: test Manual Page |
| there | use this script to determine if there are links |
usage: there [links] |
| tmp | Move a file or files to /tmp instead of deleting them - it's safer |
usage: tmp [a file to move to /tmp] |
| todo | edit a TODO file in your home or other directory |
usage: todo [.] |
| tomdate | Give the date and time in strictly decreasing order. |
usage: tomdate usage: tomdate [separation character] usage: tomdate [-u] usage: tomdate [-s] usage: tomdate [-help] usage: tomdate [-h] |
| tomdatecompare | Compare the two dates. |
usage: tomdatecompare [date1] [date2] [-notime] |
| toolkit-packing-slip | see the description in the source code | |
| toolkitcompare | Compare the version numbers of toolkit files to the script or |
usage: toolkitcompare [toolkit] [script] [delila] |
| topostscript | convert a dvi file to PostScript |
usage: topostscript document [[firstpage [lastpage]] copies] |
| tree | Recursively apply the function in to this and deeper directories. |
usage: tree [function] [any other arguments] |
| tt | see the description in the source code | |
| txt2pdf | convert the text file to LaTeX, then to pdf |
usage: txt2pdf [text file] |
| u2a |
usage: u2a [infile] [outfile] |
|
| ua | see the description in the source code | |
| ucscdna | Grab a chunk of DNA from the UCSC database. |
usage: ucscdna [database] [chromosome] [fromrange] [torange] usage: ucscdna [database] [chromosome:fromrange-torange] usage: ucscdna [chromosome:fromrange-torange] usage: ucscdna -c usage: ucscdna |
| ungooglize |
usage: ungooglize [x] |
|
| unmkcsv | Convert a csv table to space delimited ascii table. |
usage: unmkcsv [input file name] [output file name] |
| unpacktoolkit | Unpack Tom Schneider's toolkit and set it up. |
usage: unpacktoolkit |
| untarball | The tar file name can be like x.tar, x.tar.Z, or x.tar.gz |
usage: untarball [tar file name] |
| usfn | Un Space File Name: usfn [character] |
usage: usfn [character] |
| uz | see the description in the source code | |
| vc | compare version numbers of file1 and file 2 |
usage: vc [file1] [file2] |
| vernams | Get version name of the file. |
usage: vernams [file] |
| vernum.p | vernum(input: in, output: out) | Pascal program: vernum Manual Page |
| vernums | Get version number of the file. |
usage: vernums [file] |
| versave.p | versave(input: in, output: out) | Pascal program: versave Manual Page |
| vimrc | see the description in the source code | |
| vn | Give the version number of the file |
usage: vn [file] |
| wgetac | This program uses wget to grab a GenBank sequence file. |
usage: wgetac [accession number] |
| wgetas | The second usage touches the file so its date is set to now |
usage: wgetas URL filename usage: wgetas -t URL filename |
| worcha.p | worcha(fin: in, fout: out, worchap: in, output: out) | Pascal program: worcha Manual Page |
| xwbase | see the description in the source code | |
| xwbiff | see the description in the source code | |
| xwclock | see the description in the source code | |
| xwleft | see the description in the source code | |
| xwmid | see the description in the source code | |
| xwright | see the description in the source code | |
| xwtopright | see the description in the source code | |
| xwtoprightclosed | see the description in the source code | |
| xyplo.p | xyplo(xyin: in, xyout: out, xyplop: inout, xyplom: in, | Pascal program: xyplo Manual Page |
| yvp |
Find article with given year/volume/page in PubMed
WEB PAGE: yvp.html |
usage: yvp [year] [volume] [page] usage: yvp [volume] [page] usage: yvp [year] [volume] [page] [more keys] |
| yvpa | Find article with given year/volume/page in PubMed |
usage: yvpa [year] [volume] [page] usage: yvpa [volume] [page] usage: yvpa [year] [volume] [page] [another key] |
| yvpg | Guess the reference of a paper from some text and call yvp. |
usage: yvpg [string] [-] |
| yvpgt | Call yvpg with longest token as another search parameter. |
usage: yvpgt |
| yvph | Find article with given year/volume/page in PubMed-to create an html file |
usage: yvph [year] [volume] [page] > my.html usage: yvph [volume] [page] > my.html usage: yvph [year] [volume] [page] [another key] > my.html |
| yvpk | use yvp and a key from a source bibliography file |
usage: yvpk [key in bibliography] |
| zipper | zip an entire directory (or file) |
usage: zipper [directory] |
Schneider Lab
origin: 2011 Sep 03
updated: 2012Apr05_21:11:29
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