AMChalkie
commented
4 years ago I saw the same. I think it is related to missing DEV_ROOT environment variable.
Open cottrellka opened 4 years ago
AMChalkie
commented
4 years ago I saw the same. I think it is related to missing DEV_ROOT environment variable.
shalomhillelroth
commented
4 years ago Hi, Sorry for the delayed reply, @AMChalkie is right. DEV_ROOT is initialized from the environment. I looked into it online and it seems the way it's done in some cases "misbehaves". I added a conditional clause that should take care of it. Please kindly update and let me know if it fixed the problem (it work in our environment). In any DEV_ROOT should contain the directory containing the config bash.
Best, Shalom Hillel Roth
sgennadi
commented
4 years ago Hi, I tried to install now, problem still exist ... (Centos 6.9, 7.7)
Makefile:18: /make/Makefile: No such file or directory make: *** No rule to make target `/make/Makefile'. Stop.
shalomhillelroth
commented
4 years ago Hi everybody,
I'm testing now a configure and make script that should overcome these OS derived problems. It should be ready in the next couple days, I'll let you know. In the meanwhile, please kindly note that the current script requires running into the current shell (run . ./configure.sh). Best, Shalom Hillel Roth
brownmp
commented
4 years ago Hello,
I am also seeing the same issue during installation.
I get the following output when running ./configure.sh
This work is licensed under the Creative Commons Attribution-Non-Commercial-ShareAlike 4.0 International License.
To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/4.0/.
For use of the software by commercial entities, please inquire with Tel Aviv University at ramot@ramot.org.
(c) 2019 Tel Aviv University (Erez Y. Levanon, Erez.Levanon@biu.ac.il;
Eli Eisenberg, elieis@post.tau.ac.il;
Shalom Hillel Roth, shalomhillel.roth@live.biu.ac.il).
: No such file or directory
readlink: illegal option -- f
usage: readlink [-n] [file ...]
usage: dirname path
BEDTools Path Executable Test - Succeeded
BEDTools Version Test - Succeeded
SAMTools Path Executable Test - Succeeded
SAMTools Version Test - Succeeded
BAM Utils Path Executable Test - Succeeded
BAM Utils Run Test - Succeeded
BAM Utils Version Test - Succeeded
Java Path Executable Test - Succeeded
Java Run Test - Succeeded (java.version = 10.0.2)
Python 2.7 Path Executable Test - Succeeded
Python 2.7 Version Test - SucceededI believe this is still might still be an issue with the DEV_ROOT environmental variable.
I attempted to set the DEV_ROOT environmental variable to the RNAEditingIndexer repository location, but was still unsuccessful in installation.
Best, ~M. Brown
brownmp
commented
4 years ago Managed to solve the problem by setting the environmental variable DEV_ROOT with the complete path to the RNAEditingIndexer repository directory.
~ M. Brown
jalalsiddiqui
commented
4 years ago I have been trying to install it and have similar problems:
-bash-4.2$ ./configure.sh ./configure.sh: line 9: This work is licensed under the Creative Commons Attribution-Non-Commercial-ShareAlike 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/4.0/. For use of the software by commercial entities, please inquire with Tel Aviv University at ramot@ramot.org. (c) 2019 Tel Aviv University (Erez Y. Levanon, Erez.Levanon@biu.ac.il; Eli Eisenberg, elieis@post.tau.ac.il; Shalom Hillel Roth, shalomhillel.roth@live.biu.ac.il). : No such file or directory BEDTools Path Executable Test - Succeeded BEDTools Version Test - Succeeded SAMTools Path Executable Test - Succeeded SAMTools Version Test - Succeeded BAM Utils Path Executable Test - Succeeded BAM Utils Run Test - Succeeded BAM Utils Version Test - Succeeded Java Path Executable Test - Succeeded Java Run Test - Succeeded (java.version = 1.8.0) Python 2.7 Path Executable Test - Succeeded Python 2.7 Version Test - Succeeded /fs/project/PAS1348/Software/RNAEditingIndexer -bash-4.2$ make Makefile:18: /make/Makefile: No such file or directory make: *** No rule to make target `/make/Makefile'. Stop.
I am not sure what to do.
brownmp
commented
4 years ago The problem I was running into was with the DEV_ROOT variable in the configuration file. You are going to want to set this variable yourself to the location of your cloned RNAEditingIndexer repository.
~M.Brown
jalalsiddiqui
commented
4 years ago Thanks for the help. It seemed that the DEV_ROOT variable was set right. I added echo $DEV_ROOT to see if the correct path was assigned. You have to run source on the configure.sh file as:
source configure.sh
This allows these variables to be exported. After this you can run
make
The build is done. Next step will be to test
sgennadi
commented
4 years ago Error execution make
source configure.sh bash: This work is licensed under the Creative Commons Attribution-Non-Commercial-ShareAlike 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/4.0/. For use of the software by commercial entities, please inquire with Tel Aviv University at ramot@ramot.org. (c) 2019 Tel Aviv University (Erez Y. Levanon, Erez.Levanon@biu.ac.il; Eli Eisenberg, elieis@post.tau.ac.il; Shalom Hillel Roth, shalomhillel.roth@live.biu.ac.il). : No such file or directory BEDTools Path Executable Test - Succeeded BEDTools Version Test - Succeeded SAMTools Path Executable Test - Succeeded SAMTools Version Test - Succeeded BAM Utils Path Executable Test - Succeeded BAM Utils Run Test - Succeeded BAM Utils Version Test - Succeeded Java Path Executable Test - Succeeded Java Run Test - Succeeded (java.version = 1.8.0) Python 2.7 Path Executable Test - Succeeded Python 2.7 Version Test - Succeeded
[RNAEditingIndexer]# make
make: Circular /opt/software/RNAEditingIndexer/make/Makefile <- /opt/software/RNAEditingIndexer/make/Makefile dependency dropped.
/opt/software/RNAEditingIndexer/obj/EditingIndexJavaUtils/BEDGenomeIndexer.class
/opt/software/RNAEditingIndexer/src/EditingIndexJavaUtils/BEDGenomeIndexer.java:28: illegal start of type
Map<String, Map<Integer, String>> indexedGenomeAtBEDRegions = new HashMap<>();
^
/opt/software/RNAEditingIndexer/src/EditingIndexJavaUtils/BEDGenomeIndexer.java:64: illegal start of type
Map<Integer, String> newI = new TreeMap<>();
^
2 errors
make[1]: [/opt/software/RNAEditingIndexer/make/Makefile:237: /opt/software/RNAEditingIndexer/obj/EditingIndexJavaUtils/BEDGenomeIndexer.class] Error 1
/opt/software/RNAEditingIndexer/obj/EditingIndexJavaUtils/EditingIndexBEDUtils.class
/opt/software/RNAEditingIndexer/src/EditingIndexJavaUtils/EditingIndexBEDUtils.java:28: incompatible types
found : java.lang.String
required: int
switch (args[0]) {
^
/opt/software/RNAEditingIndexer/src/EditingIndexJavaUtils/BEDGenomeIndexer.java:28: illegal start of type
Map<String, Map<Integer, String>> indexedGenomeAtBEDRegions = new HashMap<>();
^
/opt/software/RNAEditingIndexer/src/EditingIndexJavaUtils/BEDGenomeIndexer.java:64: illegal start of type
Map<Integer, String> newI = new TreeMap<>();
^
/opt/software/RNAEditingIndexer/src/EditingIndexJavaUtils/BEDGenomeIndexer.java:17: cannot find symbol
symbol : class Objects
location: package java.util
import java.util.Objects;
^
/opt/software/RNAEditingIndexer/src/EditingIndexJavaUtils/PileupToCount.java:111:
zkw96
commented
3 years ago cd make
../configure.sh
vi ~/.bashrc (export DEV_ROOT=your_path_to_RNAEditingIndexer)
source ~/.bashrc
makeI will look into this and get back to you as soon as I can.
From: zkw96 @.> Sent: Thursday, June 17, 2021 10:08 AM To: a2iEditing/RNAEditingIndexer @.> Cc: Jalal K. Siddiqui @.>; Comment @.> Subject: Re: [a2iEditing/RNAEditingIndexer] Trouble with installation - make (#3)
CAUTION: External Email
A useful solusion
cd make ../configure.sh vi ~/.bashrc (export DEV_ROOT=your_path_to_RNAEditingIndexer) source ~/.bashrc make
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I am attempting to install via the instructions provided. I used git clone to download the repository. I ran configure.sh and everything succeeded (see below). I tried the make command and it came up with the following error:
Makefile:18: /make/Makefile: No such file or directory make: *** No rule to make target `/make/Makefile'. Stop.
BEDTools Path Executable Test - Succeeded BEDTools Version Test - Succeeded SAMTools Path Executable Test - Succeeded SAMTools Version Test - Succeeded BAM Utils Path Executable Test - Succeeded BAM Utils Run Test - Succeeded BAM Utils Version Test - Succeeded Java Path Executable Test - Succeeded Java Run Test - Succeeded (java.version = 1.7.0) Python 2.7 Path Executable Test - Succeeded Python 2.7 Version Test - Succeeded