Add finchtv 1.3.0, a chromatogram trace viewer.

PR:		70271
Submitted by:	Fernan Aguero <fernan (at) iib.unsam.edu.ar>

5 files changed, 208 insertions, 0 deletions

diff --git a/biology/finchtv/Makefile b/biology/finchtv/Makefile
new file mode 100644
index 000000000000..48a20f2fea8a
--- /dev/null
+++ b/biology/finchtv/Makefile
@@ -0,0 +1,39 @@
+# ex:ts=8
+# New ports collection makefile for:	FinchTV
+# Date created:		10 Aug 2004
+# Whom:	      		Fernan Aguero <fernan@iib.unsam.edu.ar>
+#
+# $FreeBSD$
+#
+
+PORTNAME=	finchtv
+PORTVERSION=	1.3.0
+CATEGORIES=	biology
+MASTER_SITES=	http://www.geospiza.com/finchtv/download/programs/linux/
+DISTNAME=	${PORTNAME}_${PORTVERSION:S/./_/g}
+
+MAINTAINER=	fernan@iib.unsam.edu.ar
+COMMENT=	A chromatogram trace viewer
+
+USE_LINUX?=	yes
+ONLY_FOR_ARCHS=	i386
+NO_BUILD=	yes
+SUB_FILES=	pkg-message
+STRIP=
+
+do-install:
+.if !defined(NOPORTDOCS)
+	@${MKDIR} ${DOCSDIR}
+	${INSTALL_DATA} ${WRKSRC}/License.txt ${DOCSDIR}
+	${INSTALL_DATA} ${WRKSRC}/ReleaseNotes.txt ${DOCSDIR}
+	${CP} -R ${WRKSRC}/Help ${DOCSDIR}
+.endif
+	@${MKDIR} ${EXAMPLESDIR}
+	${CP} -R ${WRKSRC}/SampleData/ ${EXAMPLESDIR}
+	${BRANDELF} -t Linux ${WRKSRC}/finchtv
+	${INSTALL_PROGRAM} ${WRKSRC}/finchtv ${PREFIX}/bin
+
+post-install:
+	@ ${CAT} ${PKGMESSAGE}
+
+.include <bsd.port.mk>
diff --git a/biology/finchtv/distinfo b/biology/finchtv/distinfo
new file mode 100644
index 000000000000..2a1b52f232fe
--- /dev/null
+++ b/biology/finchtv/distinfo
@@ -0,0 +1,2 @@
+MD5 (finchtv_1_3_0.tar.gz) = c02ebd1274fda3c7974b8ee53d387239
+SIZE (finchtv_1_3_0.tar.gz) = 6694746
diff --git a/biology/finchtv/files/pkg-message.in b/biology/finchtv/files/pkg-message.in
new file mode 100644
index 000000000000..717cc61aa2d6
--- /dev/null
+++ b/biology/finchtv/files/pkg-message.in
@@ -0,0 +1,15 @@
+
+----------------------------------------------------------------------------
+
+  As reported in the ReleaseNotes.txt file, the 'Online Help' menu may not 
+  work. If you need to access the FinchTV help pages/documentation see
+  below.
+
+  FinchTV Help pages are installed under
+  %%DOCSDIR%%
+  and can be accessed using the following URL:
+  file://%%DOCSDIR%%/Help/index.htm
+
+  They are also available online at http://geospiza.com/finchtv/help
+
+----------------------------------------------------------------------------
diff --git a/biology/finchtv/pkg-descr b/biology/finchtv/pkg-descr
new file mode 100644
index 000000000000..3866c7cb671c
--- /dev/null
+++ b/biology/finchtv/pkg-descr
@@ -0,0 +1,19 @@
+FinchTV is the popular way to view sequence traces on Linux, Mac OSX,
+and Windows. FinchTV is the only trace viewer that can display an entire
+trace in a scalable multi-pane view.
+
+FinchTV reads chromatogram files from the most popular formats. In
+addition to displaying a multi-color sequence above the trace, FinchTV
+displays quality values (when available). You can adjust the scale in
+both vertical and horizontal directions in either single or multipane
+views.
+
+FinchTV can:
+o print traces (on a single page or control the number of panels printed)
+o export sequences in FASTA format
+o open gzipped files
+o open files with drag and drop
+o shows additional details about the file (sample ID, run start and stop
+  times, spacing, mobility, lane number, etc.)
+
+WWW: http://www.geospiza.com/finchtv/index.htm
diff --git a/biology/finchtv/pkg-plist b/biology/finchtv/pkg-plist
new file mode 100644
index 000000000000..7adbea413d1d
--- /dev/null
+++ b/biology/finchtv/pkg-plist
@@ -0,0 +1,133 @@
+bin/finchtv
+%%PORTDOCS%%%%DOCSDIR%%/License.txt
+%%PORTDOCS%%%%DOCSDIR%%/ReleaseNotes.txt
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/B-FinchTV_Interface/ToolBars-Toolbar.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/B-FinchTV_Interface/DataViews-Multi.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/B-FinchTV_Interface/DataViews-sMenu.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/B-FinchTV_Interface/DataViews-Std.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/B-FinchTV_Interface/DataViews-ToolBar.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/B-FinchTV_Interface/DataViews-wMenu.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/B-FinchTV_Interface/ResizingTheWindow.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/B-FinchTV_Interface/ScalingTraceData.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/B-FinchTV_Interface/Toolbars-Menu.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/B-FinchTV_Interface/ContextualMenu.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/Screens/Toolsbars2.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/Screens/BaseCalls2.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/Screens/basePosNumbers.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/Screens/basePosNumbers2.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/Screens/contextualMenus.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/Screens/Edit1.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/Screens/fileOpen1.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/Screens/fileOpen2.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/Screens/GoToBase.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/Screens/Info1.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/Screens/Info2.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/Screens/InfoDetails.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/Screens/InfoGen.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/Screens/InfoSeq.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/Screens/Print.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/Screens/Print2.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/Screens/PrintOptions.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/Screens/PrintOptions2.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/Screens/QuickStart.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/Screens/Qvals1.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/Screens/Qvals2.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/Screens/rangeSelection.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/Screens/save1.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/Screens/save2.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/Screens/save3.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/Screens/Searches.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/Screens/SelectBases.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/Screens/StatusBar.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/Screens/stdWrapped1.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/Screens/stdWrapped2.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/Screens/stdWrapped3.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/Screens/stdWrapped4.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/Screens/stdWrapped5.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/Screens/stdWrapped6.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/Screens/stdWrapped7.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/Screens/stdWrapped8.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/Screens/toolbars1.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/Screens/BaseCalls1.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/C-WorkingWithYourData/SelectingBases.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/C-WorkingWithYourData/BLAST-menu.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/C-WorkingWithYourData/DisplayingData-Basecalls-Menu.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/C-WorkingWithYourData/DisplayingData-BaseCalls.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/C-WorkingWithYourData/DisplayingData-Info-Menu.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/C-WorkingWithYourData/DisplayingData-Info.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/C-WorkingWithYourData/DisplayingData-Q20.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/C-WorkingWithYourData/DisplayingData-Qualities-Menu.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/C-WorkingWithYourData/DisplayingData-Qualities.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/C-WorkingWithYourData/DisplayingData-Raw.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/C-WorkingWithYourData/DisplayingData-RawView.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/C-WorkingWithYourData/DisplayingData-RC-menu.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/C-WorkingWithYourData/DisplayingData-RC.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/C-WorkingWithYourData/EditingData.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/C-WorkingWithYourData/ExportingData.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/C-WorkingWithYourData/Info-Details.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/C-WorkingWithYourData/Info-General.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/C-WorkingWithYourData/Info-Seq.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/C-WorkingWithYourData/Navigating-Compressed.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/C-WorkingWithYourData/Navigating-Goto.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/C-WorkingWithYourData/Navigating-Menu.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/C-WorkingWithYourData/Navigating-Numbers.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/C-WorkingWithYourData/Navigating.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/C-WorkingWithYourData/OpeningChromats-Menu.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/C-WorkingWithYourData/OpeningChromats.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/C-WorkingWithYourData/PrintingTraces-Menu.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/C-WorkingWithYourData/PrintingTraces-Options-Menupng.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/C-WorkingWithYourData/PrintingTraces-OptionsDialog.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/C-WorkingWithYourData/PrintingTraces.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/C-WorkingWithYourData/Save-Menu.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/C-WorkingWithYourData/Save.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/C-WorkingWithYourData/Search-Findbox.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/C-WorkingWithYourData/Search.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/C-WorkingWithYourData/SelectingBases-Status.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/C-WorkingWithYourData/BLAST-contextual.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/A-Introduction/about.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/Geospiza-32mmHlogo.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/Geospiza-32mmHlogo.psd
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/Geospiza-lglogo.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/Geospiza-smlogo.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/HelpTitle.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/MenuLine.gif
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/Title.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/VerNum.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/finch-bulllet.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/FinchTV-cover.jpg
+%%PORTDOCS%%%%DOCSDIR%%/Help/media/FinchTV_Mac_App.png
+%%PORTDOCS%%%%DOCSDIR%%/Help/pages/A-Introduction/01-About.html
+%%PORTDOCS%%%%DOCSDIR%%/Help/pages/A-Introduction/02-Features.html
+%%PORTDOCS%%%%DOCSDIR%%/Help/pages/A-Introduction/03-QuickStart.html
+%%PORTDOCS%%%%DOCSDIR%%/Help/pages/B-FinchTV_Interface/01-DataViews.html
+%%PORTDOCS%%%%DOCSDIR%%/Help/pages/B-FinchTV_Interface/02-ScalingTraces.html
+%%PORTDOCS%%%%DOCSDIR%%/Help/pages/B-FinchTV_Interface/03-ResizingTheWindow.html
+%%PORTDOCS%%%%DOCSDIR%%/Help/pages/B-FinchTV_Interface/04-ToolBars.html
+%%PORTDOCS%%%%DOCSDIR%%/Help/pages/B-FinchTV_Interface/05-ContextualMenus.html
+%%PORTDOCS%%%%DOCSDIR%%/Help/pages/C-WorkingWithYourData/10-SavingData.html
+%%PORTDOCS%%%%DOCSDIR%%/Help/pages/C-WorkingWithYourData/02-DisplayingData.html
+%%PORTDOCS%%%%DOCSDIR%%/Help/pages/C-WorkingWithYourData/03-PrintingATrace.html
+%%PORTDOCS%%%%DOCSDIR%%/Help/pages/C-WorkingWithYourData/04-ExportingData.html
+%%PORTDOCS%%%%DOCSDIR%%/Help/pages/C-WorkingWithYourData/05-NavigatingInTraces.html
+%%PORTDOCS%%%%DOCSDIR%%/Help/pages/C-WorkingWithYourData/06-SelectingData.html
+%%PORTDOCS%%%%DOCSDIR%%/Help/pages/C-WorkingWithYourData/07-SearchingForSequences.html
+%%PORTDOCS%%%%DOCSDIR%%/Help/pages/C-WorkingWithYourData/08-BLASTSearches.html
+%%PORTDOCS%%%%DOCSDIR%%/Help/pages/C-WorkingWithYourData/09-EditingData.html
+%%PORTDOCS%%%%DOCSDIR%%/Help/pages/C-WorkingWithYourData/01-OpenFiles.html
+%%PORTDOCS%%%%DOCSDIR%%/Help/index.htm
+%%PORTDOCS%%%%DOCSDIR%%/Help/style.css
+%%EXAMPLESDIR%%/78I21_1101.y1.ab1
+%%EXAMPLESDIR%%/G33P641RB11.scf.gz
+%%EXAMPLESDIR%%/G33P771FF3.scf
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/Help/media/B-FinchTV_Interface
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/Help/media/Screens
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/Help/media/C-WorkingWithYourData
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/Help/media/A-Introduction
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/Help/media
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/Help/pages/A-Introduction
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/Help/pages/B-FinchTV_Interface
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/Help/pages/C-WorkingWithYourData
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/Help/pages
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/Help
+%%PORTDOCS%%@dirrm %%DOCSDIR%%
+@dirrm %%EXAMPLESDIR%%