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bcgsc / LINKS

⛓ Long Interval Nucleotide K-mer Scaffolder
GNU General Public License v3.0
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Unbundling bloomfilter out of the LINKS distribution tarball and more cleanup #31

Closed mmokrejs closed 2 years ago

mmokrejs commented 6 years ago

Hi, the installation procedure mentioned in https://github.com/bcgsc/LINKS/blob/master/README.md does not match contents of the https://github.com/bcgsc/LINKS/archive/v1.8.6.tar.gz file. The file contains:

drwxrwxr-x root/root         0 2018-03-13 23:17 LINKS-1.8.6/
-rw-rw-r-- root/root     35004 2018-03-13 23:17 LINKS-1.8.6/LICENSE
-rwxrwxr-x root/root     28165 2018-03-13 23:17 LINKS-1.8.6/README.md
drwxrwxr-x root/root         0 2018-03-13 23:17 LINKS-1.8.6/bin/
-rwxrwxr-x root/root     65311 2018-03-13 23:17 LINKS-1.8.6/bin/LINKS
-rw-rw-r-- root/root     65640 2018-03-13 23:17 LINKS-1.8.6/links-logo.png
drwxrwxr-x root/root         0 2018-03-13 23:17 LINKS-1.8.6/releases/
drwxrwxr-x root/root         0 2018-03-13 23:17 LINKS-1.8.6/releases/binaries/
-rw-rw-r-- root/root    717165 2018-03-13 23:17 LINKS-1.8.6/releases/binaries/links_v1-5-1.tar.gz
-rw-rw-r-- root/root    714073 2018-03-13 23:17 LINKS-1.8.6/releases/binaries/links_v1-5-2.tar.gz
-rw-rw-r-- root/root    717241 2018-03-13 23:17 LINKS-1.8.6/releases/binaries/links_v1-5.tar.gz
-rw-rw-r-- root/root   1054299 2018-03-13 23:17 LINKS-1.8.6/releases/binaries/links_v1-6-1.tar.gz
-rw-rw-r-- root/root   1052833 2018-03-13 23:17 LINKS-1.8.6/releases/binaries/links_v1-6.tar.gz
-rw-rw-r-- root/root   1060349 2018-03-13 23:17 LINKS-1.8.6/releases/binaries/links_v1-7.tar.gz
-rw-rw-r-- root/root   1062773 2018-03-13 23:17 LINKS-1.8.6/releases/binaries/links_v1-8-1.tar.gz
-rw-rw-r-- root/root   1063183 2018-03-13 23:17 LINKS-1.8.6/releases/binaries/links_v1-8-2.tar.gz
-rw-rw-r-- root/root   1062998 2018-03-13 23:17 LINKS-1.8.6/releases/binaries/links_v1-8-3.tar.gz
-rw-rw-r-- root/root   1068147 2018-03-13 23:17 LINKS-1.8.6/releases/binaries/links_v1-8-4.tar.gz
-rw-rw-r-- root/root   1075810 2018-03-13 23:17 LINKS-1.8.6/releases/binaries/links_v1-8-5.tar.gz
-rw-rw-r-- root/root    685978 2018-03-13 23:17 LINKS-1.8.6/releases/binaries/links_v1-8-6.tar.gz
-rw-rw-r-- root/root   1153831 2018-03-13 23:17 LINKS-1.8.6/releases/binaries/links_v1-8.tar.gz
drwxrwxr-x root/root         0 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.4/
-rwxrwxr-x root/root     59848 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.4/LINKS
-rw-rw-r-- root/root    432833 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.4/LINKS-readme.pdf
-rwxrwxr-x root/root     27041 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.4/LINKS-readme.txt
lrwxrwxrwx root/root         0 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.4/LINKS.pl -> LINKS
drwxrwxr-x root/root         0 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.4/test/
-rwxrwxr-x root/root       915 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.4/test/LINKSrecipe_athaliana_ectools.sh
-rwxrwxr-x root/root       915 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.4/test/LINKSrecipe_athaliana_raw.sh
-rwxrwxr-x root/root      1752 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.4/test/LINKSrecipe_pglaucaPG29-WS77111.sh
-rwxrwxr-x root/root      3088 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.4/test/runIterativeLINKS_ECK12.sh
-rwxrwxr-x root/root      3176 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.4/test/runIterativeLINKS_ECK12A2D.sh
-rwxrwxr-x root/root      3116 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.4/test/runIterativeLINKS_ECK12raw.sh
-rwxrwxr-x root/root      3528 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.4/test/runIterativeLINKS_SCS288c.sh
-rwxrwxr-x root/root      3201 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.4/test/runIterativeLINKS_SCW303.sh
-rwxrwxr-x root/root      1316 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.4/test/runIterativeLINKS_STH58.sh
-rwxrwxr-x root/root       222 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.4/test/runall.sh
-rwxrwxr-x root/root       996 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.4/test/runme_EcoliK12iterative.sh
-rwxrwxr-x root/root      1038 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.4/test/runme_EcoliK12iterativeA2D.sh
-rwxrwxr-x root/root      1030 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.4/test/runme_EcoliK12iterativeRAW.sh
-rwxrwxr-x root/root      2081 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.4/test/runme_EcoliK12single.sh
-rwxrwxr-x root/root      2466 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.4/test/runme_EcoliK12singleMPET.sh
-rwxrwxr-x root/root      1226 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.4/test/runme_ScerevisiaeS288citerative.sh
-rwxrwxr-x root/root      1226 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.4/test/runme_ScerevisiaeW303iterative.sh
-rwxrwxr-x root/root      1029 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.4/test/runme_StyphiH58iterative.sh
drwxrwxr-x root/root         0 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.4/tools/
-rwxrwxr-x root/root      1718 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.4/tools/makeMPETOutput2EQUALfiles.pl
-rwxrwxr-x root/root      3764 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.4/tools/testBloom.pl
-rwxrwxr-x root/root      4732 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.4/tools/writeBloom.pl
drwxrwxr-x root/root         0 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.5/
-rwxrwxr-x root/root     61976 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.5/LINKS
-rw-rw-r-- root/root    433249 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.5/LINKS-readme.pdf
-rwxrwxr-x root/root     27350 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.5/LINKS-readme.txt
lrwxrwxrwx root/root         0 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.5/LINKS.pl -> LINKS
-rw-rw-r-- root/root    657720 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.5/lib.tar.gz
drwxrwxr-x root/root         0 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.5/test/
-rwxrwxr-x root/root       915 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.5/test/LINKSrecipe_athaliana_ectools.sh
-rwxrwxr-x root/root       915 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.5/test/LINKSrecipe_athaliana_raw.sh
-rwxrwxr-x root/root      1752 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.5/test/LINKSrecipe_pglaucaPG29-WS77111.sh
-rwxrwxr-x root/root      3088 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.5/test/runIterativeLINKS_ECK12.sh
-rwxrwxr-x root/root      3176 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.5/test/runIterativeLINKS_ECK12A2D.sh
-rwxrwxr-x root/root      3116 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.5/test/runIterativeLINKS_ECK12raw.sh
-rwxrwxr-x root/root      3528 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.5/test/runIterativeLINKS_SCS288c.sh
-rwxrwxr-x root/root      3201 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.5/test/runIterativeLINKS_SCW303.sh
-rwxrwxr-x root/root      1316 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.5/test/runIterativeLINKS_STH58.sh
-rwxrwxr-x root/root       222 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.5/test/runall.sh
-rwxrwxr-x root/root       996 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.5/test/runme_EcoliK12iterative.sh
-rwxrwxr-x root/root      1038 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.5/test/runme_EcoliK12iterativeA2D.sh
-rwxrwxr-x root/root      1030 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.5/test/runme_EcoliK12iterativeRAW.sh
-rwxrwxr-x root/root      2081 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.5/test/runme_EcoliK12single.sh
-rwxrwxr-x root/root      2466 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.5/test/runme_EcoliK12singleMPET.sh
-rwxrwxr-x root/root      1226 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.5/test/runme_ScerevisiaeS288citerative.sh
-rwxrwxr-x root/root      1226 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.5/test/runme_ScerevisiaeW303iterative.sh
-rwxrwxr-x root/root      1029 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.5/test/runme_StyphiH58iterative.sh
drwxrwxr-x root/root         0 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.5/tools/
-rwxrwxr-x root/root      1718 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.5/tools/makeMPETOutput2EQUALfiles.pl
-rwxrwxr-x root/root      3764 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.5/tools/testBloom.pl
-rwxrwxr-x root/root      4732 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.5/tools/writeBloom.pl
drwxrwxr-x root/root         0 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.6/
-rwxrwxr-x root/root     65311 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.6/LINKS
-rwxrwxr-x root/root     65311 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.6/LINKS.pl
-rwxrwxr-x root/root     28165 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.6/README.md
-rw-rw-r-- root/root    655063 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.6/lib.tar.gz
drwxrwxr-x root/root         0 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.6/test/
-rwxrwxr-x root/root       915 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.6/test/LINKSrecipe_athaliana_ectools.sh
-rwxrwxr-x root/root       915 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.6/test/LINKSrecipe_athaliana_raw.sh
-rwxrwxr-x root/root      1752 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.6/test/LINKSrecipe_pglaucaPG29-WS77111.sh
-rwxrwxr-x root/root      3088 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.6/test/runIterativeLINKS_ECK12.sh
-rwxrwxr-x root/root      3176 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.6/test/runIterativeLINKS_ECK12A2D.sh
-rwxrwxr-x root/root      3116 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.6/test/runIterativeLINKS_ECK12raw.sh
-rwxrwxr-x root/root      3528 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.6/test/runIterativeLINKS_SCS288c.sh
-rwxrwxr-x root/root      3201 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.6/test/runIterativeLINKS_SCW303.sh
-rwxrwxr-x root/root      1316 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.6/test/runIterativeLINKS_STH58.sh
-rwxrwxr-x root/root       222 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.6/test/runall.sh
-rwxrwxr-x root/root       996 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.6/test/runme_EcoliK12iterative.sh
-rwxrwxr-x root/root      1038 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.6/test/runme_EcoliK12iterativeA2D.sh
-rwxrwxr-x root/root      1030 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.6/test/runme_EcoliK12iterativeRAW.sh
-rwxrwxr-x root/root      2081 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.6/test/runme_EcoliK12single.sh
-rwxrwxr-x root/root      2466 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.6/test/runme_EcoliK12singleMPET.sh
-rwxrwxr-x root/root      1226 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.6/test/runme_ScerevisiaeS288citerative.sh
-rwxrwxr-x root/root      1226 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.6/test/runme_ScerevisiaeW303iterative.sh
-rwxrwxr-x root/root      1029 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.6/test/runme_StyphiH58iterative.sh
drwxrwxr-x root/root         0 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.6/tools/
-rwxrwxr-x root/root      1971 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.6/tools/consolidateGraphs.pl
-rwxrwxr-x root/root      1718 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.6/tools/makeMPETOutput2EQUALfiles.pl
-rwxrwxr-x root/root      3764 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.6/tools/testBloom.pl
-rwxrwxr-x root/root      4752 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.6/tools/writeBloom.pl
-rwxrwxr-x root/root      2016 2018-03-13 23:17 LINKS-1.8.6/scaffoldsToAGP2.pl

As you can see, the bloomfilter is hidden in the libs.tar.gz file. The file itself contains even .git contents which is not really needed by the end-users.

Alsy, why LINKS 1.8.5 and 1.8.4 are included in the 1.6.8 tarball at all?

There is no symlink used for this pair:

-rwxrwxr-x root/root     65311 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.6/LINKS
-rwxrwxr-x root/root     65311 2018-03-13 23:17 LINKS-1.8.6/releases/links_v1.8.6/LINKS.pl

Anyway, woudl it be possible to move the lib/bloomfilter into a separate package with a separate version number and drop it from the LINKS tarball altogether? Would it be possible to make some conditional import of BloomFilter the step 4 in README.md shown below?

4. CHANGE the path to BloomFilter.pm in LINKS/writeBloom.pl/testBloom.pl

Thank you for your efforts.

warrenlr commented 6 years ago

hmm I see, the file at https://github.com/bcgsc/LINKS/archive/ is prepared by github and is not committed by me.

The directory structure of the LINKS projects aims to track older tarballs here:

https://github.com/bcgsc/LINKS/tree/master/releases/binaries

I believe github scrapes all under https://github.com/bcgsc/LINKS/ to create https://github.com/bcgsc/LINKS/archive/v1.8.6.tar.gz

In the release section, I would prefer that users download the package "https://github.com/bcgsc/LINKS/releases/download/v1.8.6/links_v1-8-6.tar.gz" instead of the source

mmokrejs commented 3 years ago

Hi René, I got back to this issue with 1.8.7 release ... also the perl tools scripts are missing from the current release:

$ find LINKS-1.8.7 -name \*.pl
LINKS-1.8.7/releases/links_v1.8.5/LINKS.pl
LINKS-1.8.7/releases/links_v1.8.5/tools/makeMPETOutput2EQUALfiles.pl
LINKS-1.8.7/releases/links_v1.8.5/tools/testBloom.pl
LINKS-1.8.7/releases/links_v1.8.5/tools/writeBloom.pl
LINKS-1.8.7/releases/links_v1.8.6/LINKS.pl
LINKS-1.8.7/releases/links_v1.8.6/tools/makeMPETOutput2EQUALfiles.pl
LINKS-1.8.7/releases/links_v1.8.6/tools/testBloom.pl
LINKS-1.8.7/releases/links_v1.8.6/tools/consolidateGraphs.pl
LINKS-1.8.7/releases/links_v1.8.6/tools/writeBloom.pl
LINKS-1.8.7/releases/links_v1.8.4/LINKS.pl
LINKS-1.8.7/releases/links_v1.8.4/tools/makeMPETOutput2EQUALfiles.pl
LINKS-1.8.7/releases/links_v1.8.4/tools/testBloom.pl
LINKS-1.8.7/releases/links_v1.8.4/tools/writeBloom.pl
LINKS-1.8.7/scaffoldsToAGP2.pl
$

Seems only LINKS-1.8.7/scaffoldsToAGP2.pl and LINKS-1.8.7/bin/LINKS are available for 1.8.7. I used https://github.com/bcgsc/LINKS/archive/refs/tags/v1.8.7.tar.gz as the source.

github-actions[bot] commented 2 years ago

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your interest in LINKS!