Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

[WIP] Use SSL if possible #208

Closed
wants to merge 2 commits into from
Closed

[WIP] Use SSL if possible #208

wants to merge 2 commits into from

Conversation

yhoogstrate
Copy link
Member

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

@hexylena
Copy link
Member

[Jenkins Bot] Can one of the admins sign off on testing this PR? (Security reasons, simply comment "ok to test")

nsoranzo
nsoranzo reviewed Jul 13, 2015
View reviewed changes
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;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>
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

This is wrong, must be reverted.

Copy link
Member Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Thanks!

yhoogstrate
yhoogstrate reviewed Jul 13, 2015
View reviewed changes
packages/package_monocle_1_0_0/tool_dependencies.xml
<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>
Copy link
Member Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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.

@yhoogstrate yhoogstrate mentioned this pull request Jul 17, 2015
Closed
5 tasks
@yhoogstrate yhoogstrate changed the title Use SSL if possible [WIP] Use SSL if possible Jul 17, 2015
hexylena pushed a commit that referenced this pull request Jul 17, 2015
Closes #208
4576470 
Merged in @yhoogstrate's work
@hexylena
Copy link
Member

Now part of #213

@hexylena hexylena closed this Jul 17, 2015
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers
No reviews
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
3 participants
@yhoogstrate @hexylena @nsoranzo