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[WIP] Use SSL if possible #208
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[Jenkins Bot] Can one of the admins sign off on testing this PR? (Security reasons, simply comment "ok to test") |
@@ -8,7 +8,7 @@ | |||
<source_directory>.</source_directory> | |||
<destination_directory>$INSTALL_DIR</destination_directory> | |||
</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="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> |
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This is wrong, must be reverted.
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Thanks!
<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/digest_0.6.8.tar.gz</package> |
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Many broken urls:
--2015-07-13 19:46:45-- http://cran.fhcrc.org/src/contrib/VGAM_0.9-6.tar.gz
Resolving cran.fhcrc.org (cran.fhcrc.org)... 140.107.3.21
Connecting to cran.fhcrc.org (cran.fhcrc.org)|140.107.3.21|:80... connected.
HTTP request sent, awaiting response... 404 Not Found
2015-07-13 19:46:46 ERROR 404: Not Found.
--2015-07-13 19:46:46-- http://cran.fhcrc.org/src/contrib/Rcpp_0.11.4.tar.gz
Resolving cran.fhcrc.org (cran.fhcrc.org)... 140.107.3.21
Connecting to cran.fhcrc.org (cran.fhcrc.org)|140.107.3.21|:80... connected.
HTTP request sent, awaiting response... 404 Not Found
2015-07-13 19:46:46 ERROR 404: Not Found.
--2015-07-13 19:46:46-- http://cran.fhcrc.org/src/contrib/plyr_1.8.1.tar.gz
Resolving cran.fhcrc.org (cran.fhcrc.org)... 140.107.3.21
Connecting to cran.fhcrc.org (cran.fhcrc.org)|140.107.3.21|:80... connected.
HTTP request sent, awaiting response... 404 Not Found
2015-07-13 19:46:47 ERROR 404: Not Found.
--2015-07-13 19:46:49-- http://cran.fhcrc.org/src/contrib/stringr_0.6.2.tar.gz
Resolving cran.fhcrc.org (cran.fhcrc.org)... 140.107.3.21
Connecting to cran.fhcrc.org (cran.fhcrc.org)|140.107.3.21|:80... connected.
HTTP request sent, awaiting response... 404 Not Found
2015-07-13 19:46:49 ERROR 404: Not Found.
--2015-07-13 19:46:53-- http://cran.fhcrc.org/src/contrib/colorspace_1.2-4.tar.gz
Resolving cran.fhcrc.org (cran.fhcrc.org)... 140.107.3.21
Connecting to cran.fhcrc.org (cran.fhcrc.org)|140.107.3.21|:80... connected.
HTTP request sent, awaiting response... 404 Not Found
2015-07-13 19:46:53 ERROR 404: Not Found.
--2015-07-13 19:46:55-- http://cran.fhcrc.org/src/contrib/scales_0.2.4.tar.gz
Resolving cran.fhcrc.org (cran.fhcrc.org)... 140.107.3.21
Connecting to cran.fhcrc.org (cran.fhcrc.org)|140.107.3.21|:80... connected.
HTTP request sent, awaiting response... 404 Not Found
2015-07-13 19:46:56 ERROR 404: Not Found.
--2015-07-13 19:46:58-- http://cran.fhcrc.org/src/contrib/MASS_7.3-39.tar.gz
Resolving cran.fhcrc.org (cran.fhcrc.org)... 140.107.3.21
Connecting to cran.fhcrc.org (cran.fhcrc.org)|140.107.3.21|:80... connected.
HTTP request sent, awaiting response... 404 Not Found
2015-07-13 19:46:58 ERROR 404: Not Found.
--2015-07-13 19:46:58-- http://cran.fhcrc.org/src/contrib/ggplot2_1.0.0.tar.gz
Resolving cran.fhcrc.org (cran.fhcrc.org)... 140.107.3.21
Connecting to cran.fhcrc.org (cran.fhcrc.org)|140.107.3.21|:80... connected.
HTTP request sent, awaiting response... 404 Not Found
2015-07-13 19:46:59 ERROR 404: Not Found.
--2015-07-13 19:46:59-- http://cran.fhcrc.org/src/contrib/lattice_0.20-30.tar.gz
Resolving cran.fhcrc.org (cran.fhcrc.org)... 140.107.3.21
Connecting to cran.fhcrc.org (cran.fhcrc.org)|140.107.3.21|:80... connected.
HTTP request sent, awaiting response... 404 Not Found
2015-07-13 19:46:59 ERROR 404: Not Found.
--2015-07-13 19:46:59-- http://cran.fhcrc.org/src/contrib/Matrix_1.1-5.tar.gz
Resolving cran.fhcrc.org (cran.fhcrc.org)... 140.107.3.21
Connecting to cran.fhcrc.org (cran.fhcrc.org)|140.107.3.21|:80... connected.
HTTP request sent, awaiting response... 404 Not Found
2015-07-13 19:47:00 ERROR 404: Not Found.
--2015-07-13 19:47:00-- http://cran.fhcrc.org/src/contrib/igraph_0.7.1.tar.gz
Resolving cran.fhcrc.org (cran.fhcrc.org)... 140.107.3.21
Connecting to cran.fhcrc.org (cran.fhcrc.org)|140.107.3.21|:80... connected.
HTTP request sent, awaiting response... 404 Not Found
2015-07-13 19:47:00 ERROR 404: Not Found.
--2015-07-13 19:47:00-- http://cran.fhcrc.org/src/contrib/cluster_2.0.1.tar.gz
Resolving cran.fhcrc.org (cran.fhcrc.org)... 140.107.3.21
Connecting to cran.fhcrc.org (cran.fhcrc.org)|140.107.3.21|:80... connected.
HTTP request sent, awaiting response... 404 Not Found
2015-07-13 19:47:00 ERROR 404: Not Found.
--2015-07-13 19:47:04-- http://cran.fhcrc.org/src/contrib/matrixStats_0.14.0.tar.gz
Resolving cran.fhcrc.org (cran.fhcrc.org)... 140.107.3.21
Connecting to cran.fhcrc.org (cran.fhcrc.org)|140.107.3.21|:80... connected.
HTTP request sent, awaiting response... 404 Not Found
2015-07-13 19:47:05 ERROR 404: Not Found.
--2015-07-13 19:47:05-- http://bioconductor.org/packages/3.0/bioc/src/contrib/limma_3.22.4.tar.gz
Resolving bioconductor.org (bioconductor.org)... 54.230.12.6, 54.192.14.12, 54.230.15.64, ...
Connecting to bioconductor.org (bioconductor.org)|54.230.12.6|:80... connected.
HTTP request sent, awaiting response... 404 Not Found
2015-07-13 19:47:05 ERROR 404: Not Found.
Merged in @yhoogstrate's work
Now part of #213 |
I tried to find all http:// urls in the tool_dependencies.xml in tools-iuc, downloaded them, created md5 sums, replaced http:// for https://, downloaded those as well, matched them with the md5sums, and if there was a match I replaced the XML files.
If you want an overview of the MD5sums:
https://gist.github.com/yhoogstrate/53dd27df439b40b2a44c#file-http_to_https (save as, open with a browser)
@todo: planemo shed_test whether installations still work