Reverted corrections and reverted urls that return empty files at bot…

…h http and https
galaxyproject · Jul 13, 2015 · 8eda935 · 8eda935
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diff --git a/packages/package_ballgown_1_0_3/tool_dependencies.xml b/packages/package_ballgown_1_0_3/tool_dependencies.xml
@@ -62,7 +62,7 @@
 Before using the Ballgown R package, a few preprocessing steps are necessary:
 * RNA-seq reads should be aligned to a reference genome. Any junction-aware aligner is appropriate.
 * A transcriptome should be assembled, or a reference transcriptome should be downloaded. Any assembler or download that produces a GTF file denoting the transcriptome's structure is appropriate.
-* Expression for the features in the transcriptome should be estimated. We provide software called _Tablemaker_ that does this estimation. Tablemaker calls _Cufflinks_ version 2.1.1 (<a href="https://dx.doi.org/10.1038/nbt.1621">Trapnell et al. (2010)</a>) to estimate transcript-level FPKMs, and provides several alternative expression measurements (e.g. average per-base coverage, number of mapped reads, etc.) for other features. Expression is estimated for each transcript, exon, and intron (junction) in the assembly.
+* Expression for the features in the transcriptome should be estimated. We provide software called _Tablemaker_ that does this estimation. Tablemaker calls _Cufflinks_ version 2.1.1 (<a href="http://dx.doi.org/10.1038/nbt.1621">Trapnell et al. (2010)</a>) to estimate transcript-level FPKMs, and provides several alternative expression measurements (e.g. average per-base coverage, number of mapped reads, etc.) for other features. Expression is estimated for each transcript, exon, and intron (junction) in the assembly.
 
 The Ballgown package provides functions to organize, visualize, and analyze the expression measurements for your transcriptome assembly.
 ]]>

diff --git a/packages/package_blat_35x1/tool_dependencies.xml b/packages/package_blat_35x1/tool_dependencies.xml
@@ -31,7 +31,7 @@ Git development repository: http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git
 
 Please note that the BLAT source and executables are freely available for
 academic, nonprofit and personal use. Commercial licensing information is
-available on the Kent Informatics website (https://www.kentinformatics.com/).
+available on the Kent Informatics website (http://www.kentinformatics.com/).
         </readme>
     </package>
 </tool_dependency>
diff --git a/packages/package_cd_hit_auxtools_0_5_2012_03_07_fix_dan/tool_dependencies.xml b/packages/package_cd_hit_auxtools_0_5_2012_03_07_fix_dan/tool_dependencies.xml
@@ -5,21 +5,21 @@
             <actions_group>
                 <!--
                 <actions architecture="x86_64" os="linux">
-                    <action type="download_by_url">https://depot.galaxyproject.org/package/linux/x86_64/cd-hit-auxtools/cd-hit-auxtools-0.5-2012-03-07-fix-dan-gh-0.0.1-Linux-x86_64.tgz</action>
+                    <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/cd-hit-auxtools/cd-hit-auxtools-0.5-2012-03-07-fix-dan-gh-0.0.1-Linux-x86_64.tgz</action>
                     <action type="move_directory_files">
                         <source_directory>.</source_directory>
                         <destination_directory>$INSTALL_DIR/bin</destination_directory>
                     </action>
                 </actions>
                 <actions architecture="i386" os="linux">
-                    <action type="download_by_url">https://depot.galaxyproject.org/package/linux/i386/cd-hit-auxtools/cd-hit-auxtools-0.5-2012-03-07-fix-dan-gh-0.0.1-Linux-i686.tgz</action>
+                    <action type="download_by_url">http://depot.galaxyproject.org/package/linux/i386/cd-hit-auxtools/cd-hit-auxtools-0.5-2012-03-07-fix-dan-gh-0.0.1-Linux-i686.tgz</action>
                     <action type="move_directory_files">
                         <source_directory>.</source_directory>
                         <destination_directory>$INSTALL_DIR/bin</destination_directory>
                     </action>
                 </actions>
                 <actions architecture="x86_64" os="darwin">
-                    <action type="download_by_url">https://depot.galaxyproject.org/package/darwin/x86_64/cd-hit-auxtools/cd-hit-auxtools-0.5-2012-03-07-fix-dan-gh-0.0.1-Darwin-x86_64.tgz</action>
+                    <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/x86_64/cd-hit-auxtools/cd-hit-auxtools-0.5-2012-03-07-fix-dan-gh-0.0.1-Darwin-x86_64.tgz</action>
                     <action type="move_directory_files">
                         <source_directory>.</source_directory>
                         <destination_directory>$INSTALL_DIR/bin</destination_directory>

diff --git a/packages/package_chemfp_1_1/tool_dependencies.xml b/packages/package_chemfp_1_1/tool_dependencies.xml
@@ -11,7 +11,7 @@
 
                 <!-- apply one small patched file, to support the query-format target-format commandline options
                 <action type="download_file">https://chem-fingerprints.googlecode.com/hg-history/1281bfcb470b84f5e75250dfa041345d280dde30/chemfp/commandline/simsearch.py</action>-->
-                <action type="download_file">https://share.gruenings.eu/simsearch.py</action>
+                <action type="download_file">http://share.gruenings.eu/simsearch.py</action>
                 <action type="shell_command">rm $INSTALL_DIR/lib/python/chemfp/commandline/simsearch.py</action>
                 <action type="move_file">
                     <source>simsearch.py</source>

diff --git a/packages/package_gnu_coreutils_8_21/tool_dependencies.xml b/packages/package_gnu_coreutils_8_21/tool_dependencies.xml
@@ -4,7 +4,7 @@
         <install version="1.0">
             <actions>
             <!--
-                repacked version of https://ftp.gnu.org/gnu/coreutils/coreutils-8.21.tar.xz,
+                repacked version of http://ftp.gnu.org/gnu/coreutils/coreutils-8.21.tar.xz,
                 because tarfile did not understand LZMA compression
             -->
             <action type="download_by_url">https://github.com/bgruening/download_store/raw/master/GNU/coreutils-8.21.tar.bz2</action>

diff --git a/packages/package_gnu_coreutils_8_22/tool_dependencies.xml b/packages/package_gnu_coreutils_8_22/tool_dependencies.xml
@@ -4,7 +4,7 @@
         <install version="1.0">
             <actions>
             <!--
-                repacked version of https://ftp.gnu.org/gnu/coreutils/coreutils-8.22.tar.xz,
+                repacked version of http://ftp.gnu.org/gnu/coreutils/coreutils-8.22.tar.xz,
                 because tarfile did not understand LZMA compression
             -->
             <action type="download_by_url">https://github.com/bgruening/download_store/raw/master/GNU/coreutils-8.22.tar.bz2</action>

diff --git a/packages/package_homer_4_2/tool_dependencies.xml b/packages/package_homer_4_2/tool_dependencies.xml
@@ -15,7 +15,7 @@
     <package name="homer" version="4.2">
         <install version="1.0">
             <actions>
-                <action type="download_by_url">https://biowhat.ucsd.edu/homer/homer.v4.2.zip</action>
+                <action type="download_by_url">http://biowhat.ucsd.edu/homer/homer.v4.2.zip</action>
                 <action type="set_environment_for_install">
                     <repository name="package_ghostscript_9_07" owner="iuc">
                         <package name="ghostscript" version="9.07" />
@@ -43,6 +43,6 @@
                 </action>
             </actions>
         </install>
-        <readme>Installing HOMER requires a perl environment. https://biowhat.ucsd.edu/homer/</readme>
+        <readme>Installing HOMER requires a perl environment. http://biowhat.ucsd.edu/homer/</readme>
     </package>
 </tool_dependency>
diff --git a/packages/package_monocle_1_0_0/tool_dependencies.xml b/packages/package_monocle_1_0_0/tool_dependencies.xml
@@ -10,34 +10,34 @@
                     <repository name="package_r_3_1_2" owner="iuc">
                         <package name="R" version="3.1.2" />
                     </repository>
-                    <package>https://cran.fhcrc.org/src/contrib/VGAM_0.9-6.tar.gz</package>
+                    <package>http://cran.fhcrc.org/src/contrib/VGAM_0.9-6.tar.gz</package>
                     <package>https://bioconductor.org/packages/3.0/data/experiment/src/contrib/HSMMSingleCell_1.0.0.tar.gz</package>
                     <package>https://bioconductor.org/packages/3.0/bioc/src/contrib/BiocGenerics_0.12.1.tar.gz</package>
                     <package>https://bioconductor.org/packages/3.0/bioc/src/contrib/Biobase_2.26.0.tar.gz</package>
-                    <package>https://cran.fhcrc.org/src/contrib/Rcpp_0.11.4.tar.gz</package>
-                    <package>https://cran.fhcrc.org/src/contrib/plyr_1.8.1.tar.gz</package>
+                    <package>http://cran.fhcrc.org/src/contrib/Rcpp_0.11.4.tar.gz</package>
+                    <package>http://cran.fhcrc.org/src/contrib/plyr_1.8.1.tar.gz</package>
                     <package>http://cran.fhcrc.org/src/contrib/digest_0.6.8.tar.gz</package>
                     <package>http://cran.fhcrc.org/src/contrib/gtable_0.1.2.tar.gz</package>
-                    <package>https://cran.fhcrc.org/src/contrib/stringr_0.6.2.tar.gz</package>
+                    <package>http://cran.fhcrc.org/src/contrib/stringr_0.6.2.tar.gz</package>
                     <package>http://cran.fhcrc.org/src/contrib/reshape2_1.4.1.tar.gz</package>
                     <package>http://cran.fhcrc.org/src/contrib/RColorBrewer_1.1-2.tar.gz</package>
                     <package>http://cran.fhcrc.org/src/contrib/dichromat_2.0-0.tar.gz</package>
-                    <package>https://cran.fhcrc.org/src/contrib/colorspace_1.2-4.tar.gz</package>
+                    <package>http://cran.fhcrc.org/src/contrib/colorspace_1.2-4.tar.gz</package>
                     <package>http://cran.fhcrc.org/src/contrib/munsell_0.4.2.tar.gz</package>
                     <package>http://cran.fhcrc.org/src/contrib/labeling_0.3.tar.gz</package>
-                    <package>https://cran.fhcrc.org/src/contrib/scales_0.2.4.tar.gz</package>
+                    <package>http://cran.fhcrc.org/src/contrib/scales_0.2.4.tar.gz</package>
                     <package>http://cran.fhcrc.org/src/contrib/proto_0.3-10.tar.gz</package>
-                    <package>https://cran.fhcrc.org/src/contrib/MASS_7.3-39.tar.gz</package>
-                    <package>https://cran.fhcrc.org/src/contrib/ggplot2_1.0.0.tar.gz</package>
-                    <package>https://cran.fhcrc.org/src/contrib/lattice_0.20-30.tar.gz</package>
-                    <package>https://cran.fhcrc.org/src/contrib/Matrix_1.1-5.tar.gz</package>
-                    <package>https://cran.fhcrc.org/src/contrib/igraph_0.7.1.tar.gz</package>
-                    <package>https://cran.fhcrc.org/src/contrib/cluster_2.0.1.tar.gz</package>
+                    <package>http://cran.fhcrc.org/src/contrib/MASS_7.3-39.tar.gz</package>
+                    <package>http://cran.fhcrc.org/src/contrib/ggplot2_1.0.0.tar.gz</package>
+                    <package>http://cran.fhcrc.org/src/contrib/lattice_0.20-30.tar.gz</package>
+                    <package>http://cran.fhcrc.org/src/contrib/Matrix_1.1-5.tar.gz</package>
+                    <package>http://cran.fhcrc.org/src/contrib/igraph_0.7.1.tar.gz</package>
+                    <package>http://cran.fhcrc.org/src/contrib/cluster_2.0.1.tar.gz</package>
                     <package>http://cran.fhcrc.org/src/contrib/combinat_0.0-8.tar.gz</package>
                     <package>http://cran.fhcrc.org/src/contrib/fastICA_1.2-0.tar.gz</package>
                     <package>http://cran.fhcrc.org/src/contrib/irlba_1.0.3.tar.gz</package>
-                    <package>https://cran.fhcrc.org/src/contrib/matrixStats_0.14.0.tar.gz</package>
-                    <package>https://bioconductor.org/packages/3.0/bioc/src/contrib/limma_3.22.4.tar.gz</package>
+                    <package>http://cran.fhcrc.org/src/contrib/matrixStats_0.14.0.tar.gz</package>
+                    <package>http://bioconductor.org/packages/3.0/bioc/src/contrib/limma_3.22.4.tar.gz</package>
                     <package>https://bioconductor.org/packages/3.0/bioc/src/contrib/monocle_1.0.0.tar.gz</package>
                 </action>
             </actions>

diff --git a/packages/package_openms_2_0/tool_dependencies.xml b/packages/package_openms_2_0/tool_dependencies.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <!-- ToDo can we get it easily without svn? Is this included in the final tarball? -->
-<!-- svn checkout https://svn.code.sf.net/p/open-ms/code/THIRDPARTY/SEARCHENGINES/Linux/64bit/ _searchengines -->
+<!-- svn checkout http://svn.code.sf.net/p/open-ms/code/THIRDPARTY/SEARCHENGINES/Linux/64bit/ _searchengines -->
 <tool_dependency>
     <package name="openms" version="2.0">
         <install version="1.0">

diff --git a/packages/package_perl_xml_parser_expat_2_41/tool_dependencies.xml b/packages/package_perl_xml_parser_expat_2_41/tool_dependencies.xml
@@ -11,7 +11,7 @@
                     </repository>
                    <!-- allow downloading and installing an Perl package from cpan.org-->
 
-                   <package>https://search.cpan.org/CPAN/authors/id/E/ET/ETHER/URI-1.65.tar.gz</package>
+                   <package>http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/URI-1.65.tar.gz</package>
                    <package>http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/LWP-MediaTypes-6.02.tar.gz</package>
                    <package>http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/Encode-Locale-1.03.tar.gz</package>
 

diff --git a/packages/package_r_3_1_1/tool_dependencies.xml b/packages/package_r_3_1_1/tool_dependencies.xml
@@ -4,7 +4,7 @@
         <install version="1.0">
             <actions_group>
                 <actions architecture="x86_64" os="darwin">
-                    <action type="download_by_url">https://depot.galaxyproject.org/package/darwin/x86_64/R/R-3.1.1-Darwin-x86_64.tgz</action>
+                    <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/x86_64/R/R-3.1.1-Darwin-x86_64.tgz</action>
                     <action type="move_directory_files">
                         <source_directory>.</source_directory>
                         <destination_directory>$INSTALL_DIR</destination_directory>

diff --git a/packages/package_rnashapes_2_1_6/tool_dependencies.xml b/packages/package_rnashapes_2_1_6/tool_dependencies.xml
@@ -5,31 +5,31 @@
             <actions_group>
                 <!-- Download the binaries for RNAshapes compatible with 32-bit OSX. -->
                 <actions os="darwin" architecture="i386">
-                    <action type="download_by_url">https://bibiserv.techfak.uni-bielefeld.de/spool/download/bibiserv_1383039523_10840/RNAshapes-2.1.6-osx.tar.gz</action>
+                    <action type="download_by_url">http://bibiserv.techfak.uni-bielefeld.de/spool/download/bibiserv_1383039523_10840/RNAshapes-2.1.6-osx.tar.gz</action>
                     <action type="move_file">
                         <source>RNAshapes</source>
                         <destination>$INSTALL_DIR/bin/</destination>
                     </action>
                 </actions>
                 <!-- Download the binaries for RNAshapes compatible with 32-bit Linux (i386). -->
                 <actions os="linux" architecture="i386">
-                    <action type="download_by_url">https://bibiserv.techfak.uni-bielefeld.de/spool/download/bibiserv_1383039480_10830/RNAshapes-2.1.6-i386-linux.tar.gz</action>
+                    <action type="download_by_url">http://bibiserv.techfak.uni-bielefeld.de/spool/download/bibiserv_1383039480_10830/RNAshapes-2.1.6-i386-linux.tar.gz</action>
                     <action type="move_file">
                         <source>RNAshapes</source>
                         <destination>$INSTALL_DIR/bin/</destination>
                     </action>
                 </actions>
                 <!-- Download the binaries for RNAshapes compatible with 32-bit Linux (i686). -->
                 <actions os="linux" architecture="i686">
-                    <action type="download_by_url">https://bibiserv.techfak.uni-bielefeld.de/spool/download/bibiserv_1383039480_10830/RNAshapes-2.1.6-i386-linux.tar.gz</action>
+                    <action type="download_by_url">http://bibiserv.techfak.uni-bielefeld.de/spool/download/bibiserv_1383039480_10830/RNAshapes-2.1.6-i386-linux.tar.gz</action>
                     <action type="move_file">
                         <source>RNAshapes</source>
                         <destination>$INSTALL_DIR/bin/</destination>
                     </action>
                 </actions>
                 <!-- This actions tag is only processed if none of the above tags resulted in a successful installation. -->
                 <actions>
-                    <action type="download_by_url">https://bibiserv.techfak.uni-bielefeld.de/spool/download/bibiserv_1383039313_10782/RNAshapes-2.1.6.tar.gz</action>
+                    <action type="download_by_url">http://bibiserv.techfak.uni-bielefeld.de/spool/download/bibiserv_1383039313_10782/RNAshapes-2.1.6.tar.gz</action>
                     <action type="autoconf" />
                 </actions>
                 <!-- The $PATH environment variable is only set if one of the above <actions> tags resulted in a successful installation. -->

diff --git a/packages/package_snpeff_3_6/tool_dependencies.xml b/packages/package_snpeff_3_6/tool_dependencies.xml
@@ -8,7 +8,7 @@
                     <source_directory>.</source_directory>
                     <destination_directory>$INSTALL_DIR</destination_directory>
                 </action>
-                <action type="shell_command">sed -i.orig -e 's;https://downloads.sourceforge.net/project/snpeff/databases;https://snpeff-data.galaxyproject.org/databases;g' $INSTALL_DIR/snpEff.config</action>
+                <action type="shell_command">sed -i.orig -e 's;http://downloads.sourceforge.net/project/snpeff/databases;https://snpeff-data.galaxyproject.org/databases;g' $INSTALL_DIR/snpEff.config</action>
                 <action type="set_environment">
                     <environment_variable name="SNPEFF_JAR_PATH" action="set_to">$INSTALL_DIR</environment_variable>
                 </action>

diff --git a/packages/package_snpeff_4_0/tool_dependencies.xml b/packages/package_snpeff_4_0/tool_dependencies.xml
@@ -8,7 +8,7 @@
                     <source_directory>.</source_directory>
                     <destination_directory>$INSTALL_DIR</destination_directory>
                 </action>
-                <action type="shell_command">sed -i.orig -e 's;https://downloads.sourceforge.net/project/snpeff/databases;https://snpeff-data.galaxyproject.org/databases;g' $INSTALL_DIR/snpEff.config</action>
+                <action type="shell_command">sed -i.orig -e 's;http://downloads.sourceforge.net/project/snpeff/databases;https://snpeff-data.galaxyproject.org/databases;g' $INSTALL_DIR/snpEff.config</action>
                 <action type="set_environment">
                     <environment_variable name="SNPEFF_JAR_PATH" action="set_to">$INSTALL_DIR</environment_variable>
                 </action>

diff --git a/packages/package_snpeff_4_1/tool_dependencies.xml b/packages/package_snpeff_4_1/tool_dependencies.xml
@@ -8,7 +8,7 @@
                     <source_directory>.</source_directory>
                     <destination_directory>$INSTALL_DIR</destination_directory>
                 </action>
-                <action type="shell_command">sed -i.orig -e 's;https://downloads.sourceforge.net/project/snpeff/databases;https://snpeff-data.galaxyproject.org/databases;g' $INSTALL_DIR/snpEff.config</action>
+                <action type="shell_command">sed -i.orig -e 's;http://downloads.sourceforge.net/project/snpeff/databases;https://snpeff-data.galaxyproject.org/databases;g' $INSTALL_DIR/snpEff.config</action>
                 <action type="set_environment">
                     <environment_variable name="SNPEFF_JAR_PATH" action="set_to">$INSTALL_DIR</environment_variable>
                 </action>

diff --git a/packages/package_squid_1_9g/tool_dependencies.xml b/packages/package_squid_1_9g/tool_dependencies.xml
@@ -32,7 +32,7 @@ squid code in your own work, see the files:
   LICENSE      -- version 2 of the GNU Public License (see COPYRIGHT)
 
 For a web page with more information on squid, see:
-  https://www.genetics.wustl.edu/eddy/software/#squid
+  http://www.genetics.wustl.edu/eddy/software/#squid
 
 You can always download the latest stable release of squid from:
   ftp://ftp.genetics.wustl.edu/pub/eddy/software/squid.tar.gz