Closes #208

Merged in @yhoogstrate's work
galaxyproject · Jul 17, 2015 · 4576470 · 4576470
2 parents 9d028d9 + 8eda935
commit 4576470
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diff --git a/packages/package_art_2014_11_03/tool_dependencies.xml b/packages/package_art_2014_11_03/tool_dependencies.xml
@@ -5,7 +5,7 @@
   <package name="art" version="2014_11_03">
     <install version="1.0">
       <actions>
-        <action type="download_by_url" sha256="31f172ac5953ec32e4ae7787b2aa25e62d55b086647ac1e3e6298bbe39e89645">http://www.niehs.nih.gov/research/resources/assets/docs/artsrcvanillaicecream031114linuxtgz.tgz</action>
+        <action type="download_by_url" sha256="31f172ac5953ec32e4ae7787b2aa25e62d55b086647ac1e3e6298bbe39e89645">https://www.niehs.nih.gov/research/resources/assets/docs/artsrcvanillaicecream031114linuxtgz.tgz</action>
         <action type="set_environment_for_install">
           <repository name="package_gsl_1_16" owner="iuc">
             <package name="gsl" version="1.16" />

diff --git a/packages/package_atlas_3_10/tool_dependencies.xml b/packages/package_atlas_3_10/tool_dependencies.xml
@@ -36,7 +36,7 @@
                     <!-- NOOP: On OS X we will use Apple's vecLib -->
                 </actions>
                 <actions>
-                    <action type="download_file">http://downloads.sourceforge.net/project/math-atlas/Stable/3.10.2/atlas3.10.2.tar.bz2</action>
+                    <action type="download_file">https://downloads.sourceforge.net/project/math-atlas/Stable/3.10.2/atlas3.10.2.tar.bz2</action>
                     <action type="download_file">http://www.netlib.org/lapack/lapack-3.5.0.tgz</action>
                     <action type="download_file">https://depot.galaxyproject.org/patch/atlas/static_full_blas_lapack.diff</action>
                     <action type="download_file">https://depot.galaxyproject.org/patch/atlas/shared_libraries.diff</action>

diff --git a/packages/package_atlas_3_11/tool_dependencies.xml b/packages/package_atlas_3_11/tool_dependencies.xml
@@ -3,7 +3,7 @@
         <install version="1.0">
             <actions>
                 <!-- first action is always downloading -->
-                <action target_filename="ATLAS.tar.bz2" type="download_by_url" sha256="818a4b8bbcb50878a8b1b9f71b4274d242ab46bf860c74676e98dec1d0248821">http://downloads.sourceforge.net/project/math-atlas/Developer%20%28unstable%29/3.11.11/atlas3.11.11.tar.bz2</action>
+                <action target_filename="ATLAS.tar.bz2" type="download_by_url" sha256="818a4b8bbcb50878a8b1b9f71b4274d242ab46bf860c74676e98dec1d0248821">https://downloads.sourceforge.net/project/math-atlas/Developer%20%28unstable%29/3.11.11/atlas3.11.11.tar.bz2</action>
 
                 <action type="download_file">http://www.netlib.org/lapack/lapack-3.4.2.tgz</action>
 

diff --git a/packages/package_bcftools_1_2/tool_dependencies.xml b/packages/package_bcftools_1_2/tool_dependencies.xml
@@ -6,7 +6,7 @@
         <install version="1.0">
             <actions_group>
                 <actions architecture="x86_64" os="linux">
-                    <action type="download_by_url" sha256="82d36151aebe1785c283ab0a98bf7e1714e11ee82ff5efc032fc18a33136975b">http://depot.galaxyproject.org/package/linux/x86_64/bcftools/bcftools-1.2-Linux-x86_64.tgz</action>
+                    <action type="download_by_url" sha256="82d36151aebe1785c283ab0a98bf7e1714e11ee82ff5efc032fc18a33136975b">https://depot.galaxyproject.org/package/linux/x86_64/bcftools/bcftools-1.2-Linux-x86_64.tgz</action>
                     <action type="move_directory_files">
                         <source_directory>.</source_directory>
                         <destination_directory>$INSTALL_DIR</destination_directory>

diff --git a/packages/package_bison_3_0/tool_dependencies.xml b/packages/package_bison_3_0/tool_dependencies.xml
@@ -17,7 +17,7 @@
             generalized LR (GLR) parser employing LALR(1) parser tables. As an experimental feature, Bison can also generate IELR(1) or canonical LR(1) parser tables.
             Once you are proficient with Bison, you can use it to develop a wide range of language parsers, from those used in simple desk calculators to complex programming languages.
 
-            http://www.gnu.org/software/bison/
+            https://www.gnu.org/software/bison/
         </readme>
     </package>
 </tool_dependency>
diff --git a/packages/package_blat_35x1/tool_dependencies.xml b/packages/package_blat_35x1/tool_dependencies.xml
@@ -25,7 +25,7 @@
             </actions>
         </install>
         <readme>
-BLAT sequence aligner from the UCSC: http://genome.ucsc.edu/FAQ/FAQblat.html
+BLAT sequence aligner from the UCSC: https://genome.ucsc.edu/FAQ/FAQblat.html
 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

diff --git a/packages/package_boost_1_53/tool_dependencies.xml b/packages/package_boost_1_53/tool_dependencies.xml
@@ -5,7 +5,7 @@
     <package name="boost" version="1.53.0">
         <install version="1.0">
             <actions>
-                <action type="download_by_url" sha256="818a4b8bbcb50878a8b1b9f71b4274d242ab46bf860c74676e98dec1d0248821">http://downloads.sourceforge.net/project/boost/boost/1.53.0/boost_1_53_0.tar.bz2</action>
+                <action type="download_by_url" sha256="818a4b8bbcb50878a8b1b9f71b4274d242ab46bf860c74676e98dec1d0248821">https://downloads.sourceforge.net/project/boost/boost/1.53.0/boost_1_53_0.tar.bz2</action>
 
                 <!-- populate the environment variables from the dependend repos -->
                 <action type="set_environment_for_install">

diff --git a/packages/package_boost_1_55/tool_dependencies.xml b/packages/package_boost_1_55/tool_dependencies.xml
@@ -5,7 +5,7 @@
     <package name="boost" version="1.55.0">
         <install version="1.0">
             <actions>
-                <action type="download_by_url" sha256="818a4b8bbcb50878a8b1b9f71b4274d242ab46bf860c74676e98dec1d0248821">http://downloads.sourceforge.net/project/boost/boost/1.55.0/boost_1_55_0.tar.gz</action>
+                <action type="download_by_url" sha256="818a4b8bbcb50878a8b1b9f71b4274d242ab46bf860c74676e98dec1d0248821">https://downloads.sourceforge.net/project/boost/boost/1.55.0/boost_1_55_0.tar.gz</action>
 
                 <!-- populate the environment variables from the dependend repos -->
                 <action type="set_environment_for_install">

diff --git a/packages/package_boost_1_57/tool_dependencies.xml b/packages/package_boost_1_57/tool_dependencies.xml
@@ -5,7 +5,7 @@
     <package name="boost" version="1.57">
         <install version="1.0">
             <actions>
-                <action type="download_by_url" sha256="818a4b8bbcb50878a8b1b9f71b4274d242ab46bf860c74676e98dec1d0248821">http://sourceforge.net/projects/boost/files/boost/1.57.0/boost_1_57_0.tar.gz</action>
+                <action type="download_by_url" sha256="818a4b8bbcb50878a8b1b9f71b4274d242ab46bf860c74676e98dec1d0248821">https://sourceforge.net/projects/boost/files/boost/1.57.0/boost_1_57_0.tar.gz</action>
 
                 <!-- populate the environment variables from the dependend repos -->
                 <action type="set_environment_for_install">

diff --git a/packages/package_bowtie_1_0_0/tool_dependencies.xml b/packages/package_bowtie_1_0_0/tool_dependencies.xml
@@ -2,7 +2,7 @@
     <package name="bowtie" version="1.0.0">
         <install version="1.0">
             <actions>
-                <action type="download_by_url" sha256="818a4b8bbcb50878a8b1b9f71b4274d242ab46bf860c74676e98dec1d0248821">http://downloads.sourceforge.net/project/bowtie-bio/bowtie/1.0.0/bowtie-1.0.0-src.zip</action>
+                <action type="download_by_url" sha256="818a4b8bbcb50878a8b1b9f71b4274d242ab46bf860c74676e98dec1d0248821">https://downloads.sourceforge.net/project/bowtie-bio/bowtie/1.0.0/bowtie-1.0.0-src.zip</action>
                 <action type="shell_command">make</action>
                 <action type="move_file">
                     <source>bowtie</source>

diff --git a/packages/package_bowtie_2_2_5/tool_dependencies.xml b/packages/package_bowtie_2_2_5/tool_dependencies.xml
@@ -10,7 +10,7 @@
                     </action>
                 </actions>
                 <actions>
-                    <action type="download_by_url" sha256="818a4b8bbcb50878a8b1b9f71b4274d242ab46bf860c74676e98dec1d0248821">http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.2.5/bowtie2-2.2.5-source.zip</action>
+                    <action type="download_by_url" sha256="818a4b8bbcb50878a8b1b9f71b4274d242ab46bf860c74676e98dec1d0248821">https://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.2.5/bowtie2-2.2.5-source.zip</action>
                     <action type="shell_command">make</action>
                     <action type="move_file">
                         <source>bowtie2</source>

diff --git a/packages/package_bwa_0_7_7/tool_dependencies.xml b/packages/package_bwa_0_7_7/tool_dependencies.xml
@@ -2,7 +2,7 @@
     <package name="bwa" version="0.7.7">
         <install version="1.0">
             <actions>
-                <action type="download_by_url" sha256="818a4b8bbcb50878a8b1b9f71b4274d242ab46bf860c74676e98dec1d0248821">http://downloads.sourceforge.net/project/bio-bwa/bwa-0.7.7.tar.bz2</action>
+                <action type="download_by_url" sha256="818a4b8bbcb50878a8b1b9f71b4274d242ab46bf860c74676e98dec1d0248821">https://downloads.sourceforge.net/project/bio-bwa/bwa-0.7.7.tar.bz2</action>
                 <action type="shell_command">make</action>
                 <action type="move_file">
                     <source>bwa</source>
@@ -14,4 +14,4 @@
             </actions>
         </install>
     </package>
-</tool_dependency>
+</tool_dependency>
diff --git a/packages/package_chemfp_1_1/tool_dependencies.xml b/packages/package_chemfp_1_1/tool_dependencies.xml
@@ -2,15 +2,15 @@
     <package name="chemfp" version="1.1p1">
         <install version="1.0">
             <actions>
-                <action type="download_by_url" sha256="1beb7d0d19eeac231d21d59446db117e2e4f0f31bb03af57a59d2ad2e672a482">http://chem-fingerprints.googlecode.com/files/chemfp-1.1p1.tar.gz</action>
+                <action type="download_by_url" sha256="1beb7d0d19eeac231d21d59446db117e2e4f0f31bb03af57a59d2ad2e672a482">https://chem-fingerprints.googlecode.com/files/chemfp-1.1p1.tar.gz</action>
                 <action type="make_directory">$INSTALL_DIR/lib/python</action>
                 <action type="shell_command">
                     export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
                     python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
                 </action>
 
                 <!-- apply one small patched file, to support the query-format target-format commandline options
-                <action type="download_file">http://chem-fingerprints.googlecode.com/hg-history/1281bfcb470b84f5e75250dfa041345d280dde30/chemfp/commandline/simsearch.py</action>-->
+                <action type="download_file">https://chem-fingerprints.googlecode.com/hg-history/1281bfcb470b84f5e75250dfa041345d280dde30/chemfp/commandline/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">

diff --git a/packages/package_cummerbund_2_8_2/tool_dependencies.xml b/packages/package_cummerbund_2_8_2/tool_dependencies.xml
@@ -59,18 +59,18 @@
                     <package sha256sum="1d5006429702315152e18553078505df0c5db151e39f27e658ae5fbb17316eb0">https://depot.galaxyproject.org/package/noarch/R.methodsS3_1.6.1.tar.gz</package>
                     <package sha256sum="d7a29f983705d2d9bc0a046d8d725c6e5ddaf0f6f4cd6dfa5e3d7cbf920d5f2a">https://depot.galaxyproject.org/package/noarch/matrixStats_0.12.2.tar.gz</package>
                     <package sha256sum="d451f2c72c46a7b5fa6dd252a207ba72f0a5a86d1bfc95408935f079efa85f77">https://depot.galaxyproject.org/package/noarch/BiocGenerics_0.12.1.tar.gz</package>
-                    <package sha256sum="4944c5241897a0b1271da90d4a2d56fa13c24da50aa4508500f5cd06f57954d5">http://bioarchive.galaxyproject.org/S4Vectors_0.4.0.tar.gz</package>
+                    <package sha256sum="4944c5241897a0b1271da90d4a2d56fa13c24da50aa4508500f5cd06f57954d5">https://bioarchive.galaxyproject.org/S4Vectors_0.4.0.tar.gz</package>
                     <package sha256sum="6c26fcb89570f869fe476688d59e99f4c4eb8358a4f8a16d00f77ab04a9c3db9">https://depot.galaxyproject.org/package/noarch/IRanges_2.0.1.tar.gz</package>
                     <package sha256sum="459d8904e30999435f7dd2ce40fc9a1b076982f798a6d2fb752d0311a7bcbd4b">https://depot.galaxyproject.org/package/noarch/GenomeInfoDb_1.2.4.tar.gz</package>
-                    <package sha256sum="9dd60b3ade8981ceb2d32b09d00fa297277fd64c41aa898003cc49c55bae7652">http://bioarchive.galaxyproject.org/XVector_0.6.0.tar.gz</package>
+                    <package sha256sum="9dd60b3ade8981ceb2d32b09d00fa297277fd64c41aa898003cc49c55bae7652">https://bioarchive.galaxyproject.org/XVector_0.6.0.tar.gz</package>
                     <package sha256sum="f7cb9304e22f05e61c8e2e395bfa791ef548ec209d0a9eb00129745f20677bd1">https://depot.galaxyproject.org/package/noarch/GenomicRanges_1.18.3.tar.gz</package>
-                    <package sha256sum="4b8d7f156dd533e671d6b52ea9bd641aa9e4bc27552cdcea46492a979548ad5f">http://bioarchive.galaxyproject.org/zlibbioc_1.12.0.tar.gz</package>
+                    <package sha256sum="4b8d7f156dd533e671d6b52ea9bd641aa9e4bc27552cdcea46492a979548ad5f">https://bioarchive.galaxyproject.org/zlibbioc_1.12.0.tar.gz</package>
                     <package sha256sum="b00af8f8eb1dbafa4e0ab25b571fa0a9484376c761b4de949eb6bbb7d41bd0cd">https://depot.galaxyproject.org/package/noarch/Biostrings_2.34.1.tar.gz</package>
                     <package sha256sum="c845acbc05ff87a12aec1162fe687dda1a043d3e2efa5c08902c006b1ef5f4a6">https://depot.galaxyproject.org/package/noarch/Rsamtools_1.18.2.tar.gz</package>
-                    <package sha256sum="92cd14cda4a094e8f9421a3bbe7ad6709a462106bc04a8fd59f2574c2651533d">http://bioarchive.galaxyproject.org/BiocParallel_1.0.0.tar.gz</package>
-                    <package sha256sum="7585cd13b5ae6c3dd918327803de4918dcc11cf6bea45df4e5051c492e49db2a">http://bioarchive.galaxyproject.org/Biobase_2.26.0.tar.gz</package>
+                    <package sha256sum="92cd14cda4a094e8f9421a3bbe7ad6709a462106bc04a8fd59f2574c2651533d">https://bioarchive.galaxyproject.org/BiocParallel_1.0.0.tar.gz</package>
+                    <package sha256sum="7585cd13b5ae6c3dd918327803de4918dcc11cf6bea45df4e5051c492e49db2a">https://bioarchive.galaxyproject.org/Biobase_2.26.0.tar.gz</package>
                     <package sha256sum="214a293286af854001ce46b9d866ea5b3fbc4e6b8383be0952f63491e4f6171c">https://depot.galaxyproject.org/package/noarch/AnnotationDbi_1.28.1.tar.gz</package>
-                    <package sha256sum="b309c360f6a65204e71dce65aa0c40af8b0334a5ccefe3b0a16ce438a8ebe41f">http://bioarchive.galaxyproject.org/biomaRt_2.22.0.tar.gz</package>
+                    <package sha256sum="b309c360f6a65204e71dce65aa0c40af8b0334a5ccefe3b0a16ce438a8ebe41f">https://bioarchive.galaxyproject.org/biomaRt_2.22.0.tar.gz</package>
                     <package sha256sum="eea049da0427d04a65c0a8b41a41ad1fc679a174e94b0879d5035d676e6ae3f0">https://depot.galaxyproject.org/package/noarch/GenomicAlignments_1.2.1.tar.gz</package>
                     <package sha256sum="c0284805d84f83f6189dc5a58461ea9ace8ec43dc301b0b317f4c3b493bf8bdb">https://depot.galaxyproject.org/package/noarch/rtracklayer_1.26.2.tar.gz</package>
                     <package sha256sum="fab6bf44f61353d3fdd26779768a049b22b3120e5ef53de08d9b2ffcb9eb4278">https://bioarchive.galaxyproject.org/BSgenome_1.34.0.tar.gz</package>
@@ -85,4 +85,4 @@
         <readme>
         </readme>
     </package>
-</tool_dependency>
+</tool_dependency>
diff --git a/packages/package_deseq2_1_0_17/tool_dependencies.xml b/packages/package_deseq2_1_0_17/tool_dependencies.xml
@@ -35,7 +35,7 @@
         </install>
         <readme>
         Differential gene expression analysis based on the negative binomial distribution.
-        http://www.bioconductor.org/packages/2.12/bioc/html/DESeq2.html
+        https://www.bioconductor.org/packages/2.12/bioc/html/DESeq2.html
         Ubuntu has a bug with libgfortran. To fix that create a symlink like: sudo ln -s /usr/lib/x86_64-linux-gnu/libgfortran.so.3 /usr/lib/x86_64-linux-gnu/libgfortran.so
         </readme>
     </package>

diff --git a/packages/package_deseq2_1_2_10/tool_dependencies.xml b/packages/package_deseq2_1_2_10/tool_dependencies.xml
@@ -33,7 +33,7 @@
         </install>
         <readme>
         Differential gene expression analysis based on the negative binomial distribution.
-        http://www.bioconductor.org/packages/2.12/bioc/html/DESeq2.html
+        https://www.bioconductor.org/packages/2.12/bioc/html/DESeq2.html
         Ubuntu has a bug with libgfortran. To fix that create a symlink like: sudo ln -s /usr/lib/x86_64-linux-gnu/libgfortran.so.3 /usr/lib/x86_64-linux-gnu/libgfortran.so
         </readme>
     </package>

diff --git a/packages/package_dill_0_2/tool_dependencies.xml b/packages/package_dill_0_2/tool_dependencies.xml
@@ -18,7 +18,7 @@
             </install>
             <readme>
                 The PYTHONPATH for dill can be accessed through PYTHONPATH_DILL and the binaries with PATH_DILL.
-                http://www.cacr.caltech.edu/~mmckerns/dill.htm
+                https://www.cacr.caltech.edu/~mmckerns/dill.htm
             </readme>
         </package>
 </tool_dependency>
diff --git a/packages/package_e2fsprogs_1_42_9/tool_dependencies.xml b/packages/package_e2fsprogs_1_42_9/tool_dependencies.xml
@@ -2,7 +2,7 @@
     <package name="e2fsprogs" version="1.42.9">
         <install version="1.0">
             <actions>
-                <action type="download_by_url" sha256="818a4b8bbcb50878a8b1b9f71b4274d242ab46bf860c74676e98dec1d0248821">http://downloads.sourceforge.net/project/e2fsprogs/e2fsprogs/v1.42.9/e2fsprogs-1.42.9.tar.gz</action>
+                <action type="download_by_url" sha256="818a4b8bbcb50878a8b1b9f71b4274d242ab46bf860c74676e98dec1d0248821">https://downloads.sourceforge.net/project/e2fsprogs/e2fsprogs/v1.42.9/e2fsprogs-1.42.9.tar.gz</action>
                 <action type="autoconf" />
 
                 <action type="set_environment">

diff --git a/packages/package_eigen_2_0/tool_dependencies.xml b/packages/package_eigen_2_0/tool_dependencies.xml
@@ -2,7 +2,7 @@
     <package name="eigen2" version="2.0.17">
         <install version="1.0">
             <actions>
-                <action type="download_by_url" sha256="705028db65db7c1e393cdf55018754bf0696e376603a48a33b781bc85406ff1e">http://bitbucket.org/eigen/eigen/get/2.0.17.tar.gz</action>
+                <action type="download_by_url" sha256="705028db65db7c1e393cdf55018754bf0696e376603a48a33b781bc85406ff1e">https://bitbucket.org/eigen/eigen/get/2.0.17.tar.gz</action>
                 <action type="make_directory">$INSTALL_DIR/unpacked_source</action>
                 <action type="shell_command">cp -r * $INSTALL_DIR/unpacked_source</action>
                 <action type="make_directory">build</action>

diff --git a/packages/package_eigen_3_1/tool_dependencies.xml b/packages/package_eigen_3_1/tool_dependencies.xml
@@ -2,7 +2,7 @@
     <package name="eigen3" version="3.1.3">
         <install version="1.0">
             <actions>
-                <action type="download_by_url" sha256="2ea0ba3eb9ac7ec623d8be92be4ee651191532cb311e0c979d65da9bc6c5143a">http://bitbucket.org/eigen/eigen/get/3.1.3.tar.gz</action>
+                <action type="download_by_url" sha256="2ea0ba3eb9ac7ec623d8be92be4ee651191532cb311e0c979d65da9bc6c5143a">https://bitbucket.org/eigen/eigen/get/3.1.3.tar.gz</action>
                 <action type="make_directory">$INSTALL_DIR/unpacked_source</action>
                 <action type="shell_command">cp -r * $INSTALL_DIR/unpacked_source</action>
                 <action type="make_directory">build</action>

diff --git a/packages/package_fatotwobit_35x1/tool_dependencies.xml b/packages/package_fatotwobit_35x1/tool_dependencies.xml
@@ -20,7 +20,7 @@
         </install>
         <readme>
 faToTwoBit: convert Fasta format sequence files to a dense randomly-accessable .2bit format that gfClient can use.
-http://genome.ucsc.edu/goldenPath/help/blatSpec.html
+https://genome.ucsc.edu/goldenPath/help/blatSpec.html
 
 This is a transitional package you should migrate to use packages with the name package_ucsc_tools_312 and upwards.
 

diff --git a/packages/package_fido_f63cd47b8414f87d57b8c1b713d34a04b29c7aee/tool_dependencies.xml b/packages/package_fido_f63cd47b8414f87d57b8c1b713d34a04b29c7aee/tool_dependencies.xml
@@ -24,7 +24,7 @@
         </install>
         <readme>
             Fido is a free software tool used in the area of computational proteomics. It calculates posterior probabilities for protein
-            identifications based on database searches of tandem mass spectra. The website for Fido is here: http://noble.gs.washington.edu/proj/fido/
+            identifications based on database searches of tandem mass spectra. The website for Fido is here: https://noble.gs.washington.edu/proj/fido/
         </readme>
     </package>
 </tool_dependency>
diff --git a/packages/package_freetype_2_4/tool_dependencies.xml b/packages/package_freetype_2_4/tool_dependencies.xml
@@ -2,7 +2,7 @@
     <package name="freetype" version="2.4.11">
         <install version="1.0">
             <actions>
-                <action type="download_by_url" sha256="818a4b8bbcb50878a8b1b9f71b4274d242ab46bf860c74676e98dec1d0248821">http://downloads.sourceforge.net/project/freetype/freetype2/2.4.11/freetype-2.4.11.tar.bz2</action>
+                <action type="download_by_url" sha256="818a4b8bbcb50878a8b1b9f71b4274d242ab46bf860c74676e98dec1d0248821">https://downloads.sourceforge.net/project/freetype/freetype2/2.4.11/freetype-2.4.11.tar.bz2</action>
                 <action type="shell_command">./configure --prefix=$INSTALL_DIR/freetype/</action>
                 <action type="shell_command">make</action>
                 <action type="shell_command">make install</action>

diff --git a/packages/package_gengetopt_2_22_6/tool_dependencies.xml b/packages/package_gengetopt_2_22_6/tool_dependencies.xml
@@ -12,7 +12,7 @@
         </install>
         <readme>
             Compiling GNU gengetopt requires a C compiler.
-            http://www.gnu.org/software/gengetopt/
+            https://www.gnu.org/software/gengetopt/
         </readme>
     </package>
 </tool_dependency>
diff --git a/packages/package_gfclient_35x1/tool_dependencies.xml b/packages/package_gfclient_35x1/tool_dependencies.xml
@@ -25,7 +25,7 @@
         </install>
         <readme>
 gfClient: a program that queries gfServer over the network, and then does a detailed alignment of the query sequence with regions found by gfServer.
-http://genome.ucsc.edu/goldenPath/help/blatSpec.html
+https://genome.ucsc.edu/goldenPath/help/blatSpec.html
         </readme>
     </package>
 </tool_dependency>