[gentoo-commits] proj/sci:master commit in: sci-biology/maker/, dev-java/fits/, sci-mathematics/gismo/, sci-biology/artemis/, ...

[Justin Lecher]

commit:     e0bb430dd8c078ea0aa22268eba26a47febe7b31
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Feb  3 16:55:14 2017 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Feb  5 05:18:02 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=e0bb430d

Drop all trailing whitespaces

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 dev-java/fits/fits-1.11.0-r1.ebuild                    |  2 +-
 sci-biology/AlignGraph/AlignGraph-9999.ebuild          |  2 +-
 sci-biology/TransDecoder/TransDecoder-2.0.1.ebuild     |  2 +-
 sci-biology/TransDecoder/TransDecoder-2.1.0.ebuild     |  2 +-
 sci-biology/arachne/arachne-46233.ebuild               |  4 ++--
 sci-biology/argo/argo-1.0.24.ebuild                    |  2 +-
 sci-biology/artemis/artemis-9999.ebuild                |  2 +-
 sci-biology/blue/blue-1.1.2.ebuild                     |  2 +-
 sci-biology/blue/blue-1.1.3.ebuild                     |  2 +-
 sci-biology/clview/clview-0.1.ebuild                   |  2 +-
 sci-biology/fastqc/fastqc-0.11.3.ebuild                |  2 +-
 sci-biology/ffindex/ffindex-0.9.9.6.ebuild             |  2 +-
 sci-biology/fsa/fsa-1.15.9.ebuild                      |  4 ++--
 sci-biology/maker/maker-2.31.8.ebuild                  | 14 +++++++-------
 sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild      | 12 ++++++------
 sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild      | 12 ++++++------
 sci-biology/ncbi-blast+/ncbi-blast+-2.3.0.ebuild       | 12 ++++++------
 sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild    | 12 ++++++------
 sci-biology/picard/picard-2.8.1.ebuild                 |  4 ++--
 sci-biology/pileup/pileup-0.6.ebuild                   |  2 +-
 sci-biology/prinseq-lite/prinseq-lite-0.20.4.ebuild    |  2 +-
 sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild  |  2 +-
 sci-biology/sailfish/sailfish-0.9.2.ebuild             |  2 +-
 sci-biology/somatic-sniper/somatic-sniper-1.0.4.ebuild |  2 +-
 sci-biology/tgicl/tgicl-2.1.ebuild                     |  2 +-
 sci-biology/ugene/ugene-1.20.0.ebuild                  |  2 +-
 sci-mathematics/gismo/gismo-0.8.1.ebuild               |  2 +-
 27 files changed, 56 insertions(+), 56 deletions(-)

diff --git a/dev-java/fits/fits-1.11.0-r1.ebuild b/dev-java/fits/fits-1.11.0-r1.ebuild
index 3cb228c..12d6bb2 100644
--- a/dev-java/fits/fits-1.11.0-r1.ebuild
+++ b/dev-java/fits/fits-1.11.0-r1.ebuild
@@ -47,7 +47,7 @@ java_prepare() {
 	# from http://heasarc.gsfc.nasa.gov/docs/heasarc/fits/java/v1.0/NOTE.v111.0:
 	# The source code JAR (fits_src.jar) includes a number of new classes for
 	# which the corresponding class files are not included in fits.jar.  These
-	# classes are pre-alpha versions of support for tile compressed data that 
+	# classes are pre-alpha versions of support for tile compressed data that
 	# is being developed.  Interested Users may take a look at these, but they
 	# definitely are not expected to work today.
 	rm 	src/nom/tam/image/comp/Quantizer.java \

diff --git a/sci-biology/AlignGraph/AlignGraph-9999.ebuild b/sci-biology/AlignGraph/AlignGraph-9999.ebuild
index f6ea6bb..01b81c5 100644
--- a/sci-biology/AlignGraph/AlignGraph-9999.ebuild
+++ b/sci-biology/AlignGraph/AlignGraph-9999.ebuild
@@ -31,7 +31,7 @@ RDEPEND="${DEPEND}
 	sci-biology/blat
 	sci-biology/bowtie"
 
-# AlignGraph runs the alignment steps with BLAT and Bowtie2 automatically, but both 
+# AlignGraph runs the alignment steps with BLAT and Bowtie2 automatically, but both
 # need to be installed on the system. AlignGraph’s run time is currently 23–57 min
 # per million aligned reads. In the performance tests of this study, the memory usage
 # was 36–50 GB, and it stays <100 GB even for entire mammalian genomes. These requirements

diff --git a/sci-biology/TransDecoder/TransDecoder-2.0.1.ebuild b/sci-biology/TransDecoder/TransDecoder-2.0.1.ebuild
index 9ca6b2b..04004ce 100644
--- a/sci-biology/TransDecoder/TransDecoder-2.0.1.ebuild
+++ b/sci-biology/TransDecoder/TransDecoder-2.0.1.ebuild
@@ -46,7 +46,7 @@ src_compile(){
 
 # avoid fetching 1.5TB "${S}"/pfam/Pfam-AB.hmm.bin, see
 # "Re: [Transdecoder-users] Announcement: Transdecoder release r20140704"
-# thread in archives. You can get it from 
+# thread in archives. You can get it from
 # http://downloads.sourceforge.net/project/transdecoder/Pfam-AB.hmm.bin
 
 src_install(){

diff --git a/sci-biology/TransDecoder/TransDecoder-2.1.0.ebuild b/sci-biology/TransDecoder/TransDecoder-2.1.0.ebuild
index 2a65c0c..a7a955a 100644
--- a/sci-biology/TransDecoder/TransDecoder-2.1.0.ebuild
+++ b/sci-biology/TransDecoder/TransDecoder-2.1.0.ebuild
@@ -46,7 +46,7 @@ src_compile(){
 
 # avoid fetching 1.5TB "${S}"/pfam/Pfam-AB.hmm.bin, see
 # "Re: [Transdecoder-users] Announcement: Transdecoder release r20140704"
-# thread in archives. You can get it from 
+# thread in archives. You can get it from
 # http://downloads.sourceforge.net/project/transdecoder/Pfam-AB.hmm.bin
 
 src_install(){

diff --git a/sci-biology/arachne/arachne-46233.ebuild b/sci-biology/arachne/arachne-46233.ebuild
index 2b56ae9..acc86be 100644
--- a/sci-biology/arachne/arachne-46233.ebuild
+++ b/sci-biology/arachne/arachne-46233.ebuild
@@ -29,10 +29,10 @@ src_configure() {
 
 # set the following environment variables
 # http://www.broadinstitute.org/crd/wiki/index.php/Setup
-# 
+#
 # ARACHNE_PRE
 # ARACHNE_BIN_DIR
-# ARACHNE_PRETTY_HELP 
+# ARACHNE_PRETTY_HELP
 
 pkg_postinst(){
 	einfo "Please add these to your ~/.bashrc"

diff --git a/sci-biology/argo/argo-1.0.24.ebuild b/sci-biology/argo/argo-1.0.24.ebuild
index 7670b01..57e68b1 100644
--- a/sci-biology/argo/argo-1.0.24.ebuild
+++ b/sci-biology/argo/argo-1.0.24.ebuild
@@ -11,7 +11,7 @@ HOMEPAGE="http://www.broadinstitute.org/annotation/argo2
 	http://www.broadinstitute.org/annotation/argo"
 SRC_URI="http://www.broadinstitute.org/annotation/argo/src/workspace-2008-03-11.tgz"
 #
-# cat workspace-2008-03-11/annotation/argo/version.txt 
+# cat workspace-2008-03-11/annotation/argo/version.txt
 # Gebo-1.0.17-build-1313
 
 LICENSE="LGPL-3"

diff --git a/sci-biology/artemis/artemis-9999.ebuild b/sci-biology/artemis/artemis-9999.ebuild
index 5d71760..c42eba2 100644
--- a/sci-biology/artemis/artemis-9999.ebuild
+++ b/sci-biology/artemis/artemis-9999.ebuild
@@ -34,7 +34,7 @@ DEPEND="${RDEPEND}
 	sci-biology/picard
 	dev-java/biojava"
 # some more dependencies extracted from /usr/bin/act
-# JacORB.jar, jemAlign.jar, macos.jar, chado-14-interface.jar, iBatis, biojava.jar, 
+# JacORB.jar, jemAlign.jar, macos.jar, chado-14-interface.jar, iBatis, biojava.jar,
 #
 
 # http://www.mail-archive.com/artemis-users@×××××××××.uk/msg00551.html

diff --git a/sci-biology/blue/blue-1.1.2.ebuild b/sci-biology/blue/blue-1.1.2.ebuild
index efb3480..d8b8144 100644
--- a/sci-biology/blue/blue-1.1.2.ebuild
+++ b/sci-biology/blue/blue-1.1.2.ebuild
@@ -30,7 +30,7 @@ src_install(){
 	dobin Tessel.exe GenerateMerPairs.exe Blue.exe
 	# one could install also the *.exe.so files for speedup into /usr/bin/
 
-	# The -hp option sets a flag that is checked when Blue is scanning along a read trying to find errors that could be corrected. There are a number of tests done at every base position, all based on depth of coverage. These tests will pick up random indel errors, but indels are so common at the end of homopolymer runs in 454 and IonTorrent data that multiple hp run lengths all look to be OK. For example, if our genome had AAAAAA then with Illumina data this is what we'd see almost all the time, with very rare indels at the end of the hp run resulting in runs of 5 or 7 As. With 454-like data, we'd probably get 5 As as frequently as 6 As so depth of coverage would say that neither of them are errors. The -hp flag looks out for the end of hp runs and forces an attempt at correction at that point. If the read wasn't in error, then no correction will be made. 
+	# The -hp option sets a flag that is checked when Blue is scanning along a read trying to find errors that could be corrected. There are a number of tests done at every base position, all based on depth of coverage. These tests will pick up random indel errors, but indels are so common at the end of homopolymer runs in 454 and IonTorrent data that multiple hp run lengths all look to be OK. For example, if our genome had AAAAAA then with Illumina data this is what we'd see almost all the time, with very rare indels at the end of the hp run resulting in runs of 5 or 7 As. With 454-like data, we'd probably get 5 As as frequently as 6 As so depth of coverage would say that neither of them are errors. The -hp flag looks out for the end of hp runs and forces an attempt at correction at that point. If the read wasn't in error, then no correction will be made.
 
 	# In general Blue will correct Ns - if a correct replacement can be found. The only time it doesn't do this is if there are too many consecutive Ns - as the process of finding likely replacements is combinatoric and the cost goes up exponentially with the number of consecutive Ns. In these cases, the read is abandoned and passed through uncorrected. Can you give an example of a read that you would like to see corrected differently?
 }

diff --git a/sci-biology/blue/blue-1.1.3.ebuild b/sci-biology/blue/blue-1.1.3.ebuild
index 59561cc..dcdf678 100644
--- a/sci-biology/blue/blue-1.1.3.ebuild
+++ b/sci-biology/blue/blue-1.1.3.ebuild
@@ -30,7 +30,7 @@ src_install(){
 	dobin Tessel.exe GenerateMerPairs.exe Blue.exe
 	# one could install also the *.exe.so files for speedup into /usr/bin/
 
-	# The -hp option sets a flag that is checked when Blue is scanning along a read trying to find errors that could be corrected. There are a number of tests done at every base position, all based on depth of coverage. These tests will pick up random indel errors, but indels are so common at the end of homopolymer runs in 454 and IonTorrent data that multiple hp run lengths all look to be OK. For example, if our genome had AAAAAA then with Illumina data this is what we'd see almost all the time, with very rare indels at the end of the hp run resulting in runs of 5 or 7 As. With 454-like data, we'd probably get 5 As as frequently as 6 As so depth of coverage would say that neither of them are errors. The -hp flag looks out for the end of hp runs and forces an attempt at correction at that point. If the read wasn't in error, then no correction will be made. 
+	# The -hp option sets a flag that is checked when Blue is scanning along a read trying to find errors that could be corrected. There are a number of tests done at every base position, all based on depth of coverage. These tests will pick up random indel errors, but indels are so common at the end of homopolymer runs in 454 and IonTorrent data that multiple hp run lengths all look to be OK. For example, if our genome had AAAAAA then with Illumina data this is what we'd see almost all the time, with very rare indels at the end of the hp run resulting in runs of 5 or 7 As. With 454-like data, we'd probably get 5 As as frequently as 6 As so depth of coverage would say that neither of them are errors. The -hp flag looks out for the end of hp runs and forces an attempt at correction at that point. If the read wasn't in error, then no correction will be made.
 
 	# In general Blue will correct Ns - if a correct replacement can be found. The only time it doesn't do this is if there are too many consecutive Ns - as the process of finding likely replacements is combinatoric and the cost goes up exponentially with the number of consecutive Ns. In these cases, the read is abandoned and passed through uncorrected. Can you give an example of a read that you would like to see corrected differently?
 }

diff --git a/sci-biology/clview/clview-0.1.ebuild b/sci-biology/clview/clview-0.1.ebuild
index 1e897bf..f31c048 100644
--- a/sci-biology/clview/clview-0.1.ebuild
+++ b/sci-biology/clview/clview-0.1.ebuild
@@ -58,7 +58,7 @@ SRC_URI="
 # -rw-r--r-- 1 mmokrejs mmokrejs  6941 Nov  7  2005 gcdb.h
 # -rw-r--r-- 1 mmokrejs mmokrejs  8998 Nov  7  2005 gcompress.cpp
 # -rw-r--r-- 1 mmokrejs mmokrejs  3670 Nov  7  2005 gcompress.h
-# 
+#
 
 LICENSE="Artistic"
 SLOT="0"

diff --git a/sci-biology/fastqc/fastqc-0.11.3.ebuild b/sci-biology/fastqc/fastqc-0.11.3.ebuild
index f558a75..01d3765 100644
--- a/sci-biology/fastqc/fastqc-0.11.3.ebuild
+++ b/sci-biology/fastqc/fastqc-0.11.3.ebuild
@@ -41,7 +41,7 @@ src_install(){
 	# .class files (a jar file is just a zip file full of .class files).  All
 	# you need to copy out is the contents of the bin subdirectory, the rest of
 	# the download you can discard.
-	# 
+	#
 	# jbzip2-0.9.jar comes from https://code.google.com/p/jbzip2
 	#
 	# ignore the sam-1.103.jar and rely on /usr/share/picard/lib/sam.jar from sci-biology/picard

diff --git a/sci-biology/ffindex/ffindex-0.9.9.6.ebuild b/sci-biology/ffindex/ffindex-0.9.9.6.ebuild
index 92eb117..e396426 100644
--- a/sci-biology/ffindex/ffindex-0.9.9.6.ebuild
+++ b/sci-biology/ffindex/ffindex-0.9.9.6.ebuild
@@ -44,7 +44,7 @@ src_install(){
 	#  *  Note: Bugs should be filed for the respective maintainers
 	#  *  of the package in question and not hardened@g.o.
 	#  * RWX --- --- usr/lib64/libffindex.so.0.1
-	# 
+	#
 	dolib libffindex.so.0.1 libffindex.so
 
 	# make install INSTALL_DIR="${DESTDIR}" HAVE_MPI=1

diff --git a/sci-biology/fsa/fsa-1.15.9.ebuild b/sci-biology/fsa/fsa-1.15.9.ebuild
index 71fccc8..944468f 100644
--- a/sci-biology/fsa/fsa-1.15.9.ebuild
+++ b/sci-biology/fsa/fsa-1.15.9.ebuild
@@ -24,8 +24,8 @@ RDEPEND="${DEPEND}"
 #         -C . JMF-2.1.1e/lib/jmf.jar \
 #         -C . jai-1_1_3/lib/jai_core.jar \
 #         -C . jai-1_1_3/lib/jai_codec.jar
-# * Home for VM '' does not exist: 
-# * Invalid System VM: 
+# * Home for VM '' does not exist:
+# * Invalid System VM:
 
 src_install(){
 	default

diff --git a/sci-biology/maker/maker-2.31.8.ebuild b/sci-biology/maker/maker-2.31.8.ebuild
index 58b30cf..aa566e9 100644
--- a/sci-biology/maker/maker-2.31.8.ebuild
+++ b/sci-biology/maker/maker-2.31.8.ebuild
@@ -58,22 +58,22 @@ RDEPEND="${DEPEND}"
 #                   !  Want
 #                   !  forks
 #                   !  forks::shared
-# 
+#
 # External Programs:      MISSING
 #                   !  RepeatMasker
-# 
+#
 # External C Libraries:   VERIFIED
 # MPI SUPPORT:            DISABLED
 # MWAS Web Interface:     DISABLED
 # MAKER PACKAGE:          MISSING PREREQUISITES
-# 
-# 
+#
+#
 # Important Commands:
 #         ./Build installdeps     #installs missing PERL dependencies
 #         ./Build installexes     #installs all missing external programs
 #         ./Build install         #installs MAKER
 #         ./Build status          #Shows this status menu
-# 
+#
 # Other Commands:
 #         ./Build repeatmasker    #installs RepeatMasker (asks for RepBase)
 #         ./Build blast           #installs BLAST (NCBI BLAST+)
@@ -86,7 +86,7 @@ RDEPEND="${DEPEND}"
 #         ./Build webapollo       #installs WebApollo (use maker2wap to create DBs)
 #         ./Build mpich2          #installs MPICH2 (but manual install recommended)
 # Building MAKER
-# 
+#
 # * MISSING MAKER PREREQUISITES - CANNOT CONTINUE!!
 
 S="${WORKDIR}"/maker/src
@@ -107,7 +107,7 @@ src_compile(){
 	./Build install || die
 }
 
-# If you move it, then the executables won’t be able to locate dependencies in the …/maker/data, 
+# If you move it, then the executables won’t be able to locate dependencies in the …/maker/data,
 # …/maker/lib, and …/maker/perl directories. You should really either add the location of
 # …/maker/bin to you PATH environmental variable or at most soft link the executables somewhere
 # else using the ‘ln -s’ command.

diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
index 023e89a..abf6e47 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
@@ -311,17 +311,17 @@ src_compile() {
 	# only in --with-flat-makefile configurations.  For now (12.0.0), you'll need to
 	# add or extend more DLL_LIB settings, to which end you may find the
 	# resources at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/
-	# helpful.  For instance, 
-	# 
+	# helpful.  For instance,
+	#
 	# http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/dbapi_driver.html
-	# 
+	#
 	# indicates that src/dbapi/driver/Makefile.dbapi_driver.lib should set
-	# 
+	#
 	# DLL_LIB = xncbi
-	# 
+	#
 	# (You can find the path to that makefile by examining
 	# .../status/.dbapi_driver.dep or .../build/Makefile.flat.)
-	# 
+	#
 	# To take full advantage of --with-flat-makefile, you'll need the following (instead of 'emake all_p -C "${S}"_build/build') and call configure --with-flat-makefile:
 	emake -C "${S}"_build/build -f Makefile.flat
 }

diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
index 3ac27be..4b8891b 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
@@ -314,17 +314,17 @@ src_compile() {
 	# only in --with-flat-makefile configurations.  For now (12.0.0), you'll need to
 	# add or extend more DLL_LIB settings, to which end you may find the
 	# resources at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/
-	# helpful.  For instance, 
-	# 
+	# helpful.  For instance,
+	#
 	# http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/dbapi_driver.html
-	# 
+	#
 	# indicates that src/dbapi/driver/Makefile.dbapi_driver.lib should set
-	# 
+	#
 	# DLL_LIB = xncbi
-	# 
+	#
 	# (You can find the path to that makefile by examining
 	# .../status/.dbapi_driver.dep or .../build/Makefile.flat.)
-	# 
+	#
 	# To take full advantage of --with-flat-makefile, you'll need the following (instead of 'emake all_p -C "${S}"_build/build') and call configure --with-flat-makefile:
 	emake -C "${S}"_build/build -f Makefile.flat
 }

diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.3.0.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.3.0.ebuild
index 9f04f92..93bafd4 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.3.0.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.3.0.ebuild
@@ -315,17 +315,17 @@ src_compile() {
 	# only in --with-flat-makefile configurations.  For now (12.0.0), you'll need to
 	# add or extend more DLL_LIB settings, to which end you may find the
 	# resources at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/
-	# helpful.  For instance, 
-	# 
+	# helpful.  For instance,
+	#
 	# http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/dbapi_driver.html
-	# 
+	#
 	# indicates that src/dbapi/driver/Makefile.dbapi_driver.lib should set
-	# 
+	#
 	# DLL_LIB = xncbi
-	# 
+	#
 	# (You can find the path to that makefile by examining
 	# .../status/.dbapi_driver.dep or .../build/Makefile.flat.)
-	# 
+	#
 	# To take full advantage of --with-flat-makefile, you'll need the following (instead of 'emake all_p -C "${S}"_build/build') and call configure --with-flat-makefile:
 	emake -C "${S}"_build/build -f Makefile.flat
 }

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
index 8902d3e..6ffab1b 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
@@ -316,17 +316,17 @@ src_compile() {
 	# only in --with-flat-makefile configurations.  For now (12.0.0), you'll need to
 	# add or extend more DLL_LIB settings, to which end you may find the
 	# resources at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/
-	# helpful.  For instance, 
-	# 
+	# helpful.  For instance,
+	#
 	# http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/dbapi_driver.html
-	# 
+	#
 	# indicates that src/dbapi/driver/Makefile.dbapi_driver.lib should set
-	# 
+	#
 	# DLL_LIB = xncbi
-	# 
+	#
 	# (You can find the path to that makefile by examining
 	# .../status/.dbapi_driver.dep or .../build/Makefile.flat.)
-	# 
+	#
 	# To take full advantage of --with-flat-makefile, you'll need the following (instead of 'emake all_p -C "${S}"_build/build') and call configure --with-flat-makefile:
 	emake -C "${S}"_build/build -f Makefile.flat
 	#

diff --git a/sci-biology/picard/picard-2.8.1.ebuild b/sci-biology/picard/picard-2.8.1.ebuild
index 7f8b3fd..10f350f 100644
--- a/sci-biology/picard/picard-2.8.1.ebuild
+++ b/sci-biology/picard/picard-2.8.1.ebuild
@@ -51,9 +51,9 @@ src_compile(){
 #	cd dist || die
 #	java-pkg_dojar ${PN}.jar
 #	java-pkg_dojar ${PN}-lib.jar
-#	
+#
 #	java-pkg_dolauncher ${PN} --main picard.cmdline.PicardCommandLine
-#	
+#
 #	use source && java-pkg_dosrc "${S}"/src/java/*
 #	use doc && java-pkg_dojavadoc "${S}"/javadoc
 #}

diff --git a/sci-biology/pileup/pileup-0.6.ebuild b/sci-biology/pileup/pileup-0.6.ebuild
index 260ad8a..ab2c485 100644
--- a/sci-biology/pileup/pileup-0.6.ebuild
+++ b/sci-biology/pileup/pileup-0.6.ebuild
@@ -9,7 +9,7 @@ HOMEPAGE="http://www.sanger.ac.uk/resources/software/ssaha2/"
 SRC_URI="ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/pileup.tgz"
 
 # http://samtools.sourceforge.net/pileup.shtml
-# 
+#
 LICENSE="GRL"
 SLOT="0"
 KEYWORDS=""

diff --git a/sci-biology/prinseq-lite/prinseq-lite-0.20.4.ebuild b/sci-biology/prinseq-lite/prinseq-lite-0.20.4.ebuild
index 599b428..4f62e46 100644
--- a/sci-biology/prinseq-lite/prinseq-lite-0.20.4.ebuild
+++ b/sci-biology/prinseq-lite/prinseq-lite-0.20.4.ebuild
@@ -27,7 +27,7 @@ RDEPEND="${DEPEND}
 # List::Util qw(sum min max)
 
 # prinseq-graphs.pl needs in addition
-# https://sourceforge.net/projects/prinseq/files/README.txt 
+# https://sourceforge.net/projects/prinseq/files/README.txt
 # Statistics::PCA
 
 src_install(){

diff --git a/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild b/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild
index 5cae4ae..fa347ae 100644
--- a/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild
+++ b/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild
@@ -41,7 +41,7 @@ src_configure() {
 	insinto ${VENDOR_LIB}
 	sed -e "s#/usr/perl5/lib/#${VENDOR_LIB}/#g" -i "${S}"/configure || die
 	# The below is wrong as it causes:
-	# Enter path [ /var/tmp/portage/sci-biology/repeatmasker-4.0.1-r1/work/RepeatMasker ]: 
+	# Enter path [ /var/tmp/portage/sci-biology/repeatmasker-4.0.1-r1/work/RepeatMasker ]:
 	#  -- Building monolithic RM database...sh: /var/tmp/portage/sci-biology/repeatmasker-4.0.1-r1/image///usr/share/repeatmasker/Libraries/RepeatMasker.lib: No such file or directory
 	# -e 's|> \($rmLocation/Libraries/RepeatMasker.lib\)|> '${D}'/\1|'
 	sed -i -e 's/system( "clear" );//' "${S}/configure" || die

diff --git a/sci-biology/sailfish/sailfish-0.9.2.ebuild b/sci-biology/sailfish/sailfish-0.9.2.ebuild
index 6350ef6..4138fb7 100644
--- a/sci-biology/sailfish/sailfish-0.9.2.ebuild
+++ b/sci-biology/sailfish/sailfish-0.9.2.ebuild
@@ -23,7 +23,7 @@ DEPEND="dev-libs/boost:0
 RDEPEND="${DEPEND}"
 # a C++-11 compliant compiler is needs, aka >=gcc-4.7
 
-# TODO: disable 
+# TODO: disable
 # [  7%] Performing download step (verify and extract) for 'libdivsufsort'
 #i
 # contains bundled RapMap

diff --git a/sci-biology/somatic-sniper/somatic-sniper-1.0.4.ebuild b/sci-biology/somatic-sniper/somatic-sniper-1.0.4.ebuild
index e4629b6..4478ffd 100644
--- a/sci-biology/somatic-sniper/somatic-sniper-1.0.4.ebuild
+++ b/sci-biology/somatic-sniper/somatic-sniper-1.0.4.ebuild
@@ -24,6 +24,6 @@ RDEPEND="${DEPEND}"
 
 # contains bundled copy of samtools-0.1.6 but links using a static version
 # cd /var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4_build/build/src/exe/bam-somaticsniper && /usr/bin/cmake -E cmake_link_script CMakeFiles/bam-somaticsniper.dir/link.txt --verbose=1
-# /usr/bin/x86_64-pc-linux-gnu-gcc  -Wall   -Wl,-O1 -Wl,--as-needed CMakeFiles/bam-somaticsniper.dir/main.c.o  -o ../../../../bin/bam-somaticsniper -rdynamic -lpthread -lpthread ../../lib/sniper/libsniper.a -lpthread -lm ../../../../vendor/samtools/libbam.a -lz 
+# /usr/bin/x86_64-pc-linux-gnu-gcc  -Wall   -Wl,-O1 -Wl,--as-needed CMakeFiles/bam-somaticsniper.dir/main.c.o  -o ../../../../bin/bam-somaticsniper -rdynamic -lpthread -lpthread ../../lib/sniper/libsniper.a -lpthread -lm ../../../../vendor/samtools/libbam.a -lz
 
 # contains build-common from git tree

diff --git a/sci-biology/tgicl/tgicl-2.1.ebuild b/sci-biology/tgicl/tgicl-2.1.ebuild
index 190b419..694d824 100644
--- a/sci-biology/tgicl/tgicl-2.1.ebuild
+++ b/sci-biology/tgicl/tgicl-2.1.ebuild
@@ -36,7 +36,7 @@ S="${WORKDIR}"/TGICL-2.1
 
 # Also cap3 was a problem because for a long time there was no package for it and it is not an OS product. We got author agreement that we can redistribute his binaries along with tgicl code. From what I see you have a package. It would be great if I can make tgicl depend on a cap3 package at some point. I have to check debian/rh though.
 
-# On a same note, there is a ncbi package and tgicl should depend on that. There is however a problem with mgblast. Old time ago, in a galaxy far, far away, some dark sith lord made a patch for it, patch that never made it back to ncbi developers. Meanwhile ncbi tools kept evolving and the patch is now obsolete and it may break the code. However I hope to entirely drop mgblast for the next tgicl release. I also hope to slowly phase out tclust, sclust, cdbfasta, cdbyank, zmsort, psx, tgicl_asm.psx and tgicl_cluster.psx. 
+# On a same note, there is a ncbi package and tgicl should depend on that. There is however a problem with mgblast. Old time ago, in a galaxy far, far away, some dark sith lord made a patch for it, patch that never made it back to ncbi developers. Meanwhile ncbi tools kept evolving and the patch is now obsolete and it may break the code. However I hope to entirely drop mgblast for the next tgicl release. I also hope to slowly phase out tclust, sclust, cdbfasta, cdbyank, zmsort, psx, tgicl_asm.psx and tgicl_cluster.psx.
 
 src_install(){
 	./Build install || die "Failed to execute ./Build install"

diff --git a/sci-biology/ugene/ugene-1.20.0.ebuild b/sci-biology/ugene/ugene-1.20.0.ebuild
index 99719c8..de380ef 100644
--- a/sci-biology/ugene/ugene-1.20.0.ebuild
+++ b/sci-biology/ugene/ugene-1.20.0.ebuild
@@ -17,7 +17,7 @@ IUSE="cpu_flags_x86_sse2"
 
 # http://ugene.net/download.html states Qt5.4 and QtWebkit but:
 #   Project MESSAGE: Cannot build Unipro UGENE with Qt version 4.8.7
-#   Project ERROR: Use at least Qt 5.2.1. 
+#   Project ERROR: Use at least Qt 5.2.1.
 DEPEND="
 	>=dev-qt/qtgui-5.2.1
 	>=dev-qt/qtscript-5.2.1[scripttools]"

diff --git a/sci-mathematics/gismo/gismo-0.8.1.ebuild b/sci-mathematics/gismo/gismo-0.8.1.ebuild
index f5494c6..c578f1b 100644
--- a/sci-mathematics/gismo/gismo-0.8.1.ebuild
+++ b/sci-mathematics/gismo/gismo-0.8.1.ebuild
@@ -15,7 +15,7 @@ SLOT="0"
 KEYWORDS="~amd64 ~x86"
 IUSE="doc examples"
 
-# Unbundling in progress, 
+# Unbundling in progress,
 # preparing local changes to get upstream
 DEPEND="
 	doc? ( >=app-doc/doxygen-1.8 )"