From 4b348d83d643902fa991d263b9906332bf80b25d Mon Sep 17 00:00:00 2001 From: Petar Petrov Date: Mon, 24 Apr 2017 22:03:21 +0100 Subject: [PATCH] academic/Data2FCS: Added (Data2FCS and FCS2Data). Signed-off-by: David Spencer --- academic/Data2FCS/Data2FCS.SlackBuild | 87 ++++++++++++++++++++++++++ academic/Data2FCS/Data2FCS.desktop | 8 +++ academic/Data2FCS/Data2FCS.info | 12 ++++ academic/Data2FCS/Data2FCS.png | Bin 0 -> 4239 bytes academic/Data2FCS/FCS2Data.desktop | 8 +++ academic/Data2FCS/FCS2Data.png | Bin 0 -> 4333 bytes academic/Data2FCS/README | 17 +++++ academic/Data2FCS/doinst.sh | 3 + academic/Data2FCS/slack-desc | 19 ++++++ 9 files changed, 154 insertions(+) create mode 100644 academic/Data2FCS/Data2FCS.SlackBuild create mode 100644 academic/Data2FCS/Data2FCS.desktop create mode 100644 academic/Data2FCS/Data2FCS.info create mode 100644 academic/Data2FCS/Data2FCS.png create mode 100644 academic/Data2FCS/FCS2Data.desktop create mode 100644 academic/Data2FCS/FCS2Data.png create mode 100644 academic/Data2FCS/README create mode 100644 academic/Data2FCS/doinst.sh create mode 100644 academic/Data2FCS/slack-desc diff --git a/academic/Data2FCS/Data2FCS.SlackBuild b/academic/Data2FCS/Data2FCS.SlackBuild new file mode 100644 index 0000000000..161057249d --- /dev/null +++ b/academic/Data2FCS/Data2FCS.SlackBuild @@ -0,0 +1,87 @@ +#!/bin/sh + +# Slackware build script for Data2FCS + +# Copyright 2017 Petar Petrov slackalaxy@gmail.com +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +PRGNAM=Data2FCS +PRGADD=FCS2Data +VERSION=${VERSION:-1.0} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +ARCH=noarch + +CWD=$(pwd) +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +mkdir $PRGNAM-$VERSION +cd $PRGNAM-$VERSION + +# This is Data2FCS +mkdir $PRGNAM +cd $PRGNAM +unzip $CWD/${PRGNAM}\ ${VERSION}.zip +install -D -m755 $PRGNAM.jar $PKG/usr/bin/$PRGNAM.jar + +# Rename these, so we include them as documentation +mv How\ to\ use.txt HOWTO-$PRGNAM.txt +mv Readme.txt Readme-$PRGNAM.txt + +cd .. +# This is FCS2Data +mkdir $PRGADD +cd $PRGADD +unzip $CWD/${PRGADD}\ ${VERSION}.zip +install -D -m755 $PRGADD.jar $PKG/usr/bin/$PRGADD.jar + +# Rename these, so we include them as documentation, too +mv How\ to\ use.txt HOWTO-$PRGADD.txt +mv Readme.txt Readme-$PRGADD.txt + +cd .. +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + $PRGNAM/{HOWTO-$PRGNAM.txt,Readme-$PRGNAM.txt} \ + $PRGADD/{HOWTO-$PRGADD.txt,Readme-$PRGADD.txt}\ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/usr/share/{applications,pixmaps} +cp $CWD/$PRGNAM.desktop $PKG/usr/share/applications +cp $CWD/$PRGADD.desktop $PKG/usr/share/applications +cp $CWD/$PRGNAM.png $PKG/usr/share/pixmaps +cp $CWD/$PRGADD.png $PKG/usr/share/pixmaps + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc +cat $CWD/doinst.sh > $PKG/install/doinst.sh + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} diff --git a/academic/Data2FCS/Data2FCS.desktop b/academic/Data2FCS/Data2FCS.desktop new file mode 100644 index 0000000000..4d1131896b --- /dev/null +++ b/academic/Data2FCS/Data2FCS.desktop @@ -0,0 +1,8 @@ +[Desktop Entry] +Categories=Education; +Comment=Convert ascii data into FCS +Exec=java -jar /usr/bin/Data2FCS.jar +Icon=Data2FCS +Name=Flow cytometry Data2FCS +Type=Application +GenericName= diff --git a/academic/Data2FCS/Data2FCS.info b/academic/Data2FCS/Data2FCS.info new file mode 100644 index 0000000000..3a6d0bcf0f --- /dev/null +++ b/academic/Data2FCS/Data2FCS.info @@ -0,0 +1,12 @@ +PRGNAM="Data2FCS" +VERSION="1.0" +HOMEPAGE="https://sourceforge.net/projects/data2fcs/" +DOWNLOAD="https://sourceforge.net/projects/data2fcs/files/Version%201.0/Data2FCS%201.0.zip \ + https://sourceforge.net/projects/data2fcs/files/Version%201.0/FCS2Data%201.0.zip" +MD5SUM="59b89861defa64a34ede2ea97e1194b5 \ + aa327e522bfc9b18e72f20ae1dbcdace" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="jdk" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/Data2FCS/Data2FCS.png b/academic/Data2FCS/Data2FCS.png new file mode 100644 index 0000000000000000000000000000000000000000..adaca648b25d6a20a63e71aa35c3ece8b8e82f14 GIT binary patch literal 4239 zcmZu!2{ct}8{UKt4k2+!ayW#JF-bDy2<;P+M5c?7A^S+;mQ3j&LuhwMGGxAzF}5j$ z%pxg6`yxXj%A6+7zq|ih|GM|~@3p?~d%wNj_j}&=dA@hAwWG{Tjd-|3xc~s*0goRu z$5!Q^1IK~QR;*tm0bmdx_K_Cc{NF)>h5CDJy z00ICI07zKWFRxG(Ko9_i0SE#>5Fq_OClo*t0D%D*0w53oN!Urhg#8N7L=Y5)5eR}o z5F(M7FpNSF0)jARLl6pr2xfpFip^N6OcX&87=a-e0wItDk`N{WqcDU(APkZq63m1l z6ao>D1d|{p1frM+31ot#zv5B!UuYnL{2dU2;s0S`{QMUd%jG9BhW{&hOeTV&FoIx# zAOv9^Fp5G50>Ut6Lnw-!j~O6}Vl#>POZH5JiNYuXAutF-SiUe5g-`@UV5|;^iGnDC z)dwr^rkgK_M6cA(#Y0 z015pU*8rC2-{=M)1pQY82qR1gMnMSE00v0VKg<1jM_?ubp)iPG%7Flc)%nlc00RHi z2TKw_VE};u%$*4!C;%e>1Y_40VFECUr2t?+e?5KjtZZ11P{Ct*7Vcw}_iVkzi~=Gu z9)1`w?!&ujO!p*6N>gplzT_$`L#}&~7Fy5UVHdht)}hEJAzX9TfvuylV@F55l5g5x zN9WtXZHa3^nPkWP9Dy&34LT)_Qk_rsW%k+E5MW6weRD=C>rI(}TCVjo+MD%@Rtg#~ za~RWCd(-MRw)}&jj|kr}>lAJUy$83=6W$$WRaumXyFADmqLpi>D3yCOI+bL?Pmy@m zzkNr#Znb-xb4K~RBtC{bB)hg;CcL)Gyn~iMbRceQJg8R6X8uC$DTl3VnFAr5Qw05F zoU6H_FpInT{aHIDF+cB;8;kLB)rtdiYl?b-Y+|(f z4i|xPWyaTL&H}Aj+d}7sveZln@taR5Yi;Ma7FTJ-i-Sxml<4~cb3S=+v? zLWe#3Fa=+KTSF++*#k46n;?<6LkdHDLn9L^(wIvL+aHvHqPM5iiUFp#;q@kf}+wDCPx z5i2EoN^0okOfv}_Yui@xvWs!9d6Sw+j>aBIIntdux|Xm-VdY%|T#Fgm&|NEY#Qg#J zPUUNv+ome~7L2Tc`AlAdK)Z-&fPPo5D&ksJTT4xHTl=P+lfYd*=u5{mjJYq&|MKW@ zgOc%(<*%(cA4$qqhZNQMoGX#M6OwK2q!(HhH*_3$;Abkxeq{{kt~h?cBvnQ&#l+Y( zHO@?Ibz$U_4u!|F^36Qaf-KZg&KRv{i7Wp@-BPZ`;NgigXYi{)I8zS?OHK7 z?L+bPW0!u$O8*@0HEcvZEUemn9&15qIyq}}%s@nFeU)qERQ}n^+}m+chbb~~t}plU z9)}471#iy|Mol%8CxD%o)usE~$Z1v`6~Uj#`%j#yk2f3hL^@Vd$)K!NQmB}#kZBLa zoj1IvoNT$faQdog$sHNZk>g?>yx{)M!d3eG)0IieU4HkC;8&6i;K*P zEDzU~=1U5;FE<8#eRr4Xj`{-$Gd2F?LRL{Cy`wz#^=pna)7@$9$q|~nGnWZ{s~7Es zQBBlz+mEkxP%7o#C07xBx!>|cA}E2&t-?$q{Y&KiL*C+BFKD{k(su4siBRQ_AmQDH zE&034kIsfu-t$B$L>#mU1l=&u2_j1eMd@=my zO;?6aP=JfR9#_*vWm3P$G;99!SUt2(r@*yOwKWL;l;^y@n|`_xqG zl@@neJGX*-bz%bkyS6~uQN_|2#nyATm1Erx4w)X4joa3?g+md}=9}bhIjh0oP;Fk*KIF%K2EkHJR01wuoh!2i+96wXd4g6 zbYH3%tgulcx_BJB<`zjQ2s_R9$m+gQMz}cE0L>GHt|Ej8IzBMum}ow(Kt*ihRrDh> zS$;aFX5ZY#w^yE(cLh|5Yy)!)jRCwf9l*AO66x+lz_$i@g~kkop7bvhc) z(=u_B(k~q+X>&m#hoL0xa%VX?=B}cE^y(R1D}(cdHtr)AL(M2*FGTZ8=^iO;ca|H{ z-iPb>(kX^xq14>iLtGe-mkMH?2>VFHTM1#Lxb?@Mixcup%4W^&AHwsePv%!L%)ewW zFNeuQOB#1KtMTN(#zs5C<``6y(y}r`sK)<8jak1+6l?3J-VNg$Hx09|yV}YU`zU%> z(j&{ok{+I6z{jWOUa?T+z9%PGCmnRKCjOx?B&Sd_?P1Dr_y66$qcYD<{&{>)_yfCQ zi5v+osfs~kHx~a)W5{}G27f0K@qWu z-poqB<9GDJEyl|wEpHUpvc%qB3hlN|aQ}D?Rc}~abzpwIrt@u9D&@J%V#9Yu?}o23 zca>~itPRE5u_=8fxs}yNP&`mskB0j+R)0dQy}I~B-ROBW(dFJFi?g1U@{0DgYl}l; 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Data can be easily visualized to identify +correlations and subpopulations. Subpopulations can be selected and +analysed separately. However, such software requires data in the FCS +data standard. + +This contains two programs: Data2FCS and FCS2Data. + +Data2FCS a simple application for converting data in ascii file format +into FCS3.1 files. A special treat is the possibility to transform +categorical data into numerical data. The resulting FCS data file can be +analysed in regular flow cytometry softwares, such as the open source +FCSaylzer (also available at SlackBuilds.org). + +FCS2Data is a simple application for converting FCS data files into +ascii file format. These files contain the single event data of the FCS +files, so that the data can be used in other applications. diff --git a/academic/Data2FCS/doinst.sh b/academic/Data2FCS/doinst.sh new file mode 100644 index 0000000000..5fb28930db --- /dev/null +++ b/academic/Data2FCS/doinst.sh @@ -0,0 +1,3 @@ +if [ -x /usr/bin/update-desktop-database ]; then + /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1 +fi diff --git a/academic/Data2FCS/slack-desc b/academic/Data2FCS/slack-desc new file mode 100644 index 0000000000..c46ad928f0 --- /dev/null +++ b/academic/Data2FCS/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +Data2FCS: Data2FCS (Data2FCS and FCS2Data) +Data2FCS: +Data2FCS: Data2FCS converts data from ascii files to FCS data files. The +Data2FCS: resulting FCS data file can be analysed in regular flow cytometry +Data2FCS: softwares +Data2FCS: +Data2FCS: FCS2Data is a simple application for converting FCS data files +Data2FCS: into ascii file format. These files contain the single event data +Data2FCS: of the FCS files, so that the data can be used in other +Data2FCS: applications. +Data2FCS: